Starting phenix.real_space_refine on Tue Sep 24 16:10:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/09_2024/5u1c_8481.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/09_2024/5u1c_8481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/09_2024/5u1c_8481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/09_2024/5u1c_8481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/09_2024/5u1c_8481.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/09_2024/5u1c_8481.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 92 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5188 2.51 5 N 1534 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8596 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1975 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 10, 'TRANS': 240} Chain breaks: 1 Chain: "B" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1362 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 3 Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 162 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "E" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1975 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 10, 'TRANS': 240} Chain breaks: 1 Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1362 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 3 Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 162 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "I" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 319 SG CYS A 40 21.270 47.273 39.306 1.00 11.69 S ATOM 342 SG CYS A 43 24.958 47.314 38.194 1.00 10.21 S ATOM 4615 SG CYS C 40 65.198 83.727 39.295 1.00 12.83 S ATOM 4638 SG CYS C 43 61.511 83.683 38.178 1.00 11.35 S Time building chain proxies: 5.40, per 1000 atoms: 0.63 Number of scatterers: 8596 At special positions: 0 Unit cell: (87.77, 132.31, 83.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 28 16.00 P 92 15.00 Mg 2 11.99 O 1750 8.00 N 1534 7.00 C 5188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 777.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb=" ZN C 500 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 500 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 40 " Number of angles added : 4 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 46.8% alpha, 18.7% beta 42 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.585A pdb=" N ASP A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.604A pdb=" N LYS A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 166 removed outlier: 3.868A pdb=" N GLN A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.959A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.564A pdb=" N LYS B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 171 through 186 removed outlier: 3.593A pdb=" N ALA B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 204 removed outlier: 3.506A pdb=" N ILE B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 16 removed outlier: 3.585A pdb=" N ASP C 6 " --> pdb=" O LEU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 123 through 133 removed outlier: 3.604A pdb=" N LYS C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 148 through 166 removed outlier: 3.866A pdb=" N GLN C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.959A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 93 through 108 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 123 through 134 removed outlier: 3.564A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 171 through 186 removed outlier: 3.593A pdb=" N ALA D 175 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.507A pdb=" N ILE D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 4.114A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TRP A 61 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL A 113 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 227 Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.427A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS A 244 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 88 removed outlier: 6.722A pdb=" N TRP B 61 " --> pdb=" O HIS B 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 261 removed outlier: 6.357A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 89 removed outlier: 4.114A pdb=" N VAL C 72 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TRP C 61 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL C 113 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 227 Processing sheet with id=AA8, first strand: chain 'C' and resid 240 through 244 removed outlier: 6.427A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS C 244 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 88 removed outlier: 6.722A pdb=" N TRP D 61 " --> pdb=" O HIS D 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 257 through 261 removed outlier: 6.357A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2023 1.33 - 1.45: 2224 1.45 - 1.57: 4499 1.57 - 1.69: 180 1.69 - 1.81: 40 Bond restraints: 8966 Sorted by residual: bond pdb=" C GLY A 118 " pdb=" N SER A 119 " ideal model delta sigma weight residual 1.334 1.381 -0.047 1.20e-02 6.94e+03 1.56e+01 bond pdb=" C THR A 122 " pdb=" N SER A 123 " ideal model delta sigma weight residual 1.330 1.293 0.038 1.30e-02 5.92e+03 8.33e+00 bond pdb=" C1' DT E 28 " pdb=" N1 DT E 28 " ideal model delta sigma weight residual 1.490 1.548 -0.058 3.00e-02 1.11e+03 3.69e+00 bond pdb=" C1' DT I 28 " pdb=" N1 DT I 28 " ideal model delta sigma weight residual 1.490 1.547 -0.057 3.00e-02 1.11e+03 3.63e+00 bond pdb=" C4' DC H 6 " pdb=" C3' DC H 6 " ideal model delta sigma weight residual 1.523 1.560 -0.037 2.00e-02 2.50e+03 3.47e+00 ... (remaining 8961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 12133 2.28 - 4.57: 353 4.57 - 6.85: 25 6.85 - 9.13: 1 9.13 - 11.41: 4 Bond angle restraints: 12516 Sorted by residual: angle pdb=" O GLY C 118 " pdb=" C GLY C 118 " pdb=" N SER C 119 " ideal model delta sigma weight residual 122.70 111.29 11.41 1.30e+00 5.92e-01 7.71e+01 angle pdb=" O GLY A 118 " pdb=" C GLY A 118 " pdb=" N SER A 119 " ideal model delta sigma weight residual 122.70 111.62 11.08 1.30e+00 5.92e-01 7.26e+01 angle pdb=" CA GLY C 118 " pdb=" C GLY C 118 " pdb=" N SER C 119 " ideal model delta sigma weight residual 116.69 127.81 -11.12 2.04e+00 2.40e-01 2.97e+01 angle pdb=" CA GLY A 118 " pdb=" C GLY A 118 " pdb=" N SER A 119 " ideal model delta sigma weight residual 116.69 127.67 -10.98 2.04e+00 2.40e-01 2.90e+01 angle pdb=" C GLY C 118 " pdb=" N SER C 119 " pdb=" CA SER C 119 " ideal model delta sigma weight residual 120.79 127.08 -6.29 1.39e+00 5.18e-01 2.05e+01 ... (remaining 12511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 4642 33.72 - 67.44: 418 67.44 - 101.15: 10 101.15 - 134.87: 0 134.87 - 168.59: 2 Dihedral angle restraints: 5072 sinusoidal: 2656 harmonic: 2416 Sorted by residual: dihedral pdb=" CA GLN A 148 " pdb=" C GLN A 148 " pdb=" N GLY A 149 " pdb=" CA GLY A 149 " ideal model delta harmonic sigma weight residual 180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLN C 148 " pdb=" C GLN C 148 " pdb=" N GLY C 149 " pdb=" CA GLY C 149 " ideal model delta harmonic sigma weight residual -180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA SER C 195 " pdb=" C SER C 195 " pdb=" N ALA C 196 " pdb=" CA ALA C 196 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 5069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 861 0.045 - 0.091: 394 0.091 - 0.136: 110 0.136 - 0.182: 21 0.182 - 0.227: 2 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA LYS C 46 " pdb=" N LYS C 46 " pdb=" C LYS C 46 " pdb=" CB LYS C 46 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LYS A 46 " pdb=" N LYS A 46 " pdb=" C LYS A 46 " pdb=" CB LYS A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 89 " pdb=" N ILE A 89 " pdb=" C ILE A 89 " pdb=" CB ILE A 89 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 1385 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC F 20 " -0.014 2.00e-02 2.50e+03 1.47e-02 4.87e+00 pdb=" N1 DC F 20 " 0.013 2.00e-02 2.50e+03 pdb=" C2 DC F 20 " -0.031 2.00e-02 2.50e+03 pdb=" O2 DC F 20 " 0.022 2.00e-02 2.50e+03 pdb=" N3 DC F 20 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC F 20 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC F 20 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC F 20 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC F 20 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 20 " 0.014 2.00e-02 2.50e+03 1.45e-02 4.73e+00 pdb=" N1 DC J 20 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DC J 20 " 0.030 2.00e-02 2.50e+03 pdb=" O2 DC J 20 " -0.021 2.00e-02 2.50e+03 pdb=" N3 DC J 20 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC J 20 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 20 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC J 20 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC J 20 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 19 " -0.026 2.00e-02 2.50e+03 1.43e-02 4.62e+00 pdb=" N1 DC I 19 " 0.033 2.00e-02 2.50e+03 pdb=" C2 DC I 19 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 19 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC I 19 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC I 19 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 19 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC I 19 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 19 " 0.002 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 64 2.55 - 3.14: 6733 3.14 - 3.73: 13641 3.73 - 4.31: 19417 4.31 - 4.90: 30282 Nonbonded interactions: 70137 Sorted by model distance: nonbonded pdb=" O ARG A 228 " pdb=" OD1 ASP A 229 " model vdw 1.964 3.040 nonbonded pdb=" O ARG C 228 " pdb=" OD1 ASP C 229 " model vdw 1.965 3.040 nonbonded pdb=" OD2 ASP A 64 " pdb="MG MG A 501 " model vdw 1.976 2.170 nonbonded pdb=" OD2 ASP C 64 " pdb="MG MG C 501 " model vdw 1.977 2.170 nonbonded pdb=" OG1 THR A 93 " pdb=" OP1 DC F 30 " model vdw 2.051 3.040 ... (remaining 70132 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'H' } 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 group one per residue 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: 0.380 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.910 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 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 : 0.008 0.058 8966 Z= 0.478 Angle : 0.912 11.414 12516 Z= 0.545 Chirality : 0.054 0.227 1388 Planarity : 0.005 0.035 1258 Dihedral : 20.206 168.589 3512 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.43 % 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: -4.03 (0.24), residues: 822 helix: -2.67 (0.22), residues: 320 sheet: -2.02 (0.34), residues: 194 loop : -2.86 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 235 HIS 0.014 0.002 HIS B 183 PHE 0.024 0.003 PHE C 121 TYR 0.020 0.003 TYR B 99 ARG 0.007 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 271 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8554 (mt) cc_final: 0.8226 (tp) REVERT: A 85 GLU cc_start: 0.7344 (tp30) cc_final: 0.7080 (tp30) REVERT: C 22 MET cc_start: 0.7141 (mtm) cc_final: 0.6867 (mtp) REVERT: C 60 ILE cc_start: 0.8428 (mt) cc_final: 0.8197 (tp) REVERT: C 85 GLU cc_start: 0.7345 (tp30) cc_final: 0.6977 (tp30) outliers start: 2 outliers final: 0 residues processed: 273 average time/residue: 0.2580 time to fit residues: 89.8163 Evaluate side-chains 134 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS B 114 HIS ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN C 183 HIS C 252 GLN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8966 Z= 0.345 Angle : 0.696 6.269 12516 Z= 0.393 Chirality : 0.046 0.155 1388 Planarity : 0.006 0.056 1258 Dihedral : 26.466 179.872 1916 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.55 % Allowed : 12.93 % Favored : 83.52 % 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: -2.01 (0.26), residues: 822 helix: -0.89 (0.24), residues: 340 sheet: -0.81 (0.34), residues: 210 loop : -2.10 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 61 HIS 0.009 0.001 HIS B 183 PHE 0.019 0.002 PHE C 181 TYR 0.018 0.002 TYR A 99 ARG 0.006 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 0.814 Fit side-chains REVERT: A 178 MET cc_start: 0.8103 (mtt) cc_final: 0.6214 (mtt) REVERT: A 230 SER cc_start: 0.7060 (m) cc_final: 0.6683 (t) REVERT: B 132 TRP cc_start: 0.8335 (t60) cc_final: 0.7608 (t60) REVERT: C 178 MET cc_start: 0.8102 (mtt) cc_final: 0.6174 (mtt) REVERT: C 230 SER cc_start: 0.7014 (m) cc_final: 0.6650 (t) REVERT: D 132 TRP cc_start: 0.8358 (t60) cc_final: 0.7674 (t60) outliers start: 25 outliers final: 14 residues processed: 177 average time/residue: 0.2190 time to fit residues: 51.9438 Evaluate side-chains 128 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 184 ASN B 114 HIS C 171 HIS C 184 ASN C 252 GLN D 114 HIS D 177 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8966 Z= 0.194 Angle : 0.602 8.448 12516 Z= 0.338 Chirality : 0.043 0.156 1388 Planarity : 0.004 0.034 1258 Dihedral : 26.401 178.891 1916 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.41 % Allowed : 15.77 % Favored : 81.82 % 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: -0.88 (0.28), residues: 822 helix: 0.18 (0.26), residues: 352 sheet: -0.19 (0.35), residues: 210 loop : -1.84 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 132 HIS 0.008 0.001 HIS D 183 PHE 0.012 0.001 PHE A 100 TYR 0.013 0.002 TYR A 99 ARG 0.005 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.835 Fit side-chains REVERT: A 178 MET cc_start: 0.8079 (mtt) cc_final: 0.6299 (mtt) REVERT: A 230 SER cc_start: 0.6915 (m) cc_final: 0.6567 (t) REVERT: A 269 ARG cc_start: 0.4540 (tmt170) cc_final: 0.4318 (tpt90) REVERT: B 132 TRP cc_start: 0.8339 (t60) cc_final: 0.7918 (t60) REVERT: C 178 MET cc_start: 0.8116 (mtt) cc_final: 0.6472 (mtt) REVERT: C 230 SER cc_start: 0.6899 (m) cc_final: 0.6552 (t) REVERT: D 132 TRP cc_start: 0.8324 (t60) cc_final: 0.7633 (t60) outliers start: 17 outliers final: 12 residues processed: 151 average time/residue: 0.1959 time to fit residues: 41.2252 Evaluate side-chains 122 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN B 114 HIS C 184 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN D 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 8966 Z= 0.341 Angle : 0.665 5.889 12516 Z= 0.376 Chirality : 0.046 0.147 1388 Planarity : 0.005 0.087 1258 Dihedral : 26.851 179.708 1916 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.84 % Allowed : 16.48 % Favored : 79.69 % 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: -0.61 (0.28), residues: 822 helix: 0.49 (0.26), residues: 340 sheet: -0.06 (0.36), residues: 210 loop : -1.74 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 61 HIS 0.010 0.002 HIS B 183 PHE 0.024 0.002 PHE D 100 TYR 0.019 0.003 TYR C 143 ARG 0.005 0.001 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.840 Fit side-chains REVERT: A 178 MET cc_start: 0.8326 (mtt) cc_final: 0.7028 (mtt) REVERT: B 83 TYR cc_start: 0.7280 (t80) cc_final: 0.6929 (t80) REVERT: B 132 TRP cc_start: 0.8441 (t60) cc_final: 0.7744 (t60) REVERT: C 178 MET cc_start: 0.8372 (mtt) cc_final: 0.7257 (mtt) REVERT: C 191 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7446 (mm) REVERT: D 132 TRP cc_start: 0.8456 (t60) cc_final: 0.7777 (t60) outliers start: 27 outliers final: 17 residues processed: 148 average time/residue: 0.1969 time to fit residues: 40.4899 Evaluate side-chains 134 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN C 51 HIS C 184 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8966 Z= 0.210 Angle : 0.584 5.519 12516 Z= 0.333 Chirality : 0.042 0.167 1388 Planarity : 0.004 0.053 1258 Dihedral : 26.678 179.370 1916 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.69 % Allowed : 19.89 % Favored : 76.42 % 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: -0.27 (0.29), residues: 822 helix: 0.68 (0.26), residues: 352 sheet: 0.10 (0.37), residues: 214 loop : -1.53 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.004 0.001 HIS A 12 PHE 0.011 0.001 PHE C 181 TYR 0.012 0.002 TYR C 99 ARG 0.006 0.001 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.900 Fit side-chains REVERT: A 178 MET cc_start: 0.8161 (mtt) cc_final: 0.7950 (mtt) REVERT: A 194 TYR cc_start: 0.6803 (m-80) cc_final: 0.6577 (m-80) REVERT: A 269 ARG cc_start: 0.3994 (tpt90) cc_final: 0.3726 (tpt170) REVERT: B 83 TYR cc_start: 0.7280 (t80) cc_final: 0.6973 (t80) REVERT: B 232 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7368 (m-30) outliers start: 26 outliers final: 18 residues processed: 138 average time/residue: 0.2050 time to fit residues: 39.3068 Evaluate side-chains 127 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN B 168 GLN C 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8966 Z= 0.309 Angle : 0.635 5.542 12516 Z= 0.360 Chirality : 0.045 0.187 1388 Planarity : 0.004 0.048 1258 Dihedral : 26.971 179.747 1916 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.26 % Allowed : 20.88 % Favored : 74.86 % 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: -0.35 (0.29), residues: 822 helix: 0.73 (0.26), residues: 338 sheet: 0.06 (0.37), residues: 210 loop : -1.62 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 132 HIS 0.005 0.001 HIS C 12 PHE 0.013 0.002 PHE C 121 TYR 0.021 0.002 TYR D 83 ARG 0.004 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.853 Fit side-chains outliers start: 30 outliers final: 22 residues processed: 137 average time/residue: 0.2042 time to fit residues: 38.2618 Evaluate side-chains 128 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 51 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN A 184 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8966 Z= 0.184 Angle : 0.592 8.438 12516 Z= 0.332 Chirality : 0.043 0.238 1388 Planarity : 0.004 0.034 1258 Dihedral : 26.708 179.853 1916 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.98 % Allowed : 22.87 % Favored : 74.15 % 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 (0.29), residues: 822 helix: 0.90 (0.27), residues: 352 sheet: 0.12 (0.36), residues: 220 loop : -1.83 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 132 HIS 0.004 0.001 HIS A 12 PHE 0.019 0.001 PHE B 100 TYR 0.018 0.001 TYR B 83 ARG 0.005 0.001 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.931 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 127 average time/residue: 0.1741 time to fit residues: 32.3442 Evaluate side-chains 117 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8966 Z= 0.195 Angle : 0.600 11.153 12516 Z= 0.335 Chirality : 0.042 0.179 1388 Planarity : 0.004 0.034 1258 Dihedral : 26.659 178.851 1916 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.27 % Allowed : 21.73 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 822 helix: 1.01 (0.27), residues: 350 sheet: 0.27 (0.38), residues: 206 loop : -1.70 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 132 HIS 0.004 0.001 HIS A 51 PHE 0.020 0.001 PHE B 100 TYR 0.012 0.001 TYR B 83 ARG 0.006 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.838 Fit side-chains REVERT: A 66 THR cc_start: 0.9254 (t) cc_final: 0.9018 (m) REVERT: A 181 PHE cc_start: 0.8382 (t80) cc_final: 0.8171 (t80) outliers start: 23 outliers final: 16 residues processed: 125 average time/residue: 0.1596 time to fit residues: 29.6340 Evaluate side-chains 119 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8966 Z= 0.198 Angle : 0.613 9.534 12516 Z= 0.345 Chirality : 0.043 0.155 1388 Planarity : 0.004 0.034 1258 Dihedral : 26.470 179.018 1916 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.41 % Allowed : 23.01 % Favored : 74.57 % 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: -0.07 (0.29), residues: 822 helix: 0.98 (0.26), residues: 350 sheet: 0.25 (0.38), residues: 206 loop : -1.63 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 132 HIS 0.005 0.001 HIS A 51 PHE 0.009 0.001 PHE A 121 TYR 0.018 0.001 TYR B 83 ARG 0.005 0.001 ARG C 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.789 Fit side-chains REVERT: A 66 THR cc_start: 0.9249 (t) cc_final: 0.9002 (m) REVERT: A 178 MET cc_start: 0.7923 (mtt) cc_final: 0.7583 (mtp) REVERT: A 181 PHE cc_start: 0.8413 (t80) cc_final: 0.8183 (t80) REVERT: B 83 TYR cc_start: 0.6892 (t80) cc_final: 0.6608 (t80) REVERT: C 178 MET cc_start: 0.7635 (mtt) cc_final: 0.7222 (mtp) REVERT: D 100 PHE cc_start: 0.6954 (t80) cc_final: 0.6303 (t80) outliers start: 17 outliers final: 17 residues processed: 110 average time/residue: 0.1602 time to fit residues: 26.3988 Evaluate side-chains 114 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8966 Z= 0.329 Angle : 0.684 9.100 12516 Z= 0.385 Chirality : 0.046 0.152 1388 Planarity : 0.004 0.036 1258 Dihedral : 26.655 179.164 1916 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.56 % Allowed : 23.01 % Favored : 74.43 % 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: -0.48 (0.29), residues: 822 helix: 0.70 (0.26), residues: 338 sheet: -0.14 (0.36), residues: 220 loop : -1.73 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 132 HIS 0.005 0.002 HIS A 12 PHE 0.013 0.002 PHE A 121 TYR 0.025 0.002 TYR B 83 ARG 0.004 0.001 ARG A 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.851 Fit side-chains REVERT: A 178 MET cc_start: 0.8112 (mtt) cc_final: 0.7807 (mtp) REVERT: C 178 MET cc_start: 0.7992 (mtt) cc_final: 0.7654 (mtp) REVERT: C 191 ILE cc_start: 0.7894 (mm) cc_final: 0.7670 (mm) outliers start: 18 outliers final: 16 residues processed: 111 average time/residue: 0.1726 time to fit residues: 27.7656 Evaluate side-chains 110 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 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 184 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096443 restraints weight = 21366.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.098524 restraints weight = 12652.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099862 restraints weight = 9072.785| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8966 Z= 0.206 Angle : 0.623 8.942 12516 Z= 0.351 Chirality : 0.043 0.157 1388 Planarity : 0.004 0.035 1258 Dihedral : 26.430 179.807 1916 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.98 % Allowed : 23.72 % Favored : 73.30 % 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 (0.29), residues: 822 helix: 0.83 (0.26), residues: 350 sheet: 0.12 (0.38), residues: 206 loop : -1.60 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 132 HIS 0.004 0.001 HIS C 51 PHE 0.017 0.002 PHE D 100 TYR 0.021 0.002 TYR D 83 ARG 0.004 0.001 ARG A 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1658.69 seconds wall clock time: 30 minutes 24.83 seconds (1824.83 seconds total)