Starting phenix.real_space_refine on Wed Feb 14 04:12:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/02_2024/5u1c_8481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/02_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_8481/02_2024/5u1c_8481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/02_2024/5u1c_8481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/02_2024/5u1c_8481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1c_8481/02_2024/5u1c_8481.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: 5.14, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 3.45 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: 2.65 Time building geometry restraints manager: 4.12 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: 97.82 - 105.08: 472 105.08 - 112.34: 4631 112.34 - 119.60: 3162 119.60 - 126.86: 3866 126.86 - 134.11: 385 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 2.440 ... (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 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.900 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.120 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- 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 : 0.876 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: 0.2719 time to fit residues: 94.3561 Evaluate side-chains 134 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 4.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 183 HIS B 177 GLN C 144 ASN C 183 HIS C 252 GLN ** 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: 0.7217 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8966 Z= 0.284 Angle : 0.656 6.558 12516 Z= 0.369 Chirality : 0.044 0.151 1388 Planarity : 0.005 0.049 1258 Dihedral : 26.353 179.682 1916 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.26 % Allowed : 11.79 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.27), residues: 822 helix: -0.78 (0.24), residues: 336 sheet: -1.00 (0.34), residues: 222 loop : -1.88 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 61 HIS 0.008 0.001 HIS B 183 PHE 0.018 0.002 PHE C 181 TYR 0.021 0.002 TYR A 99 ARG 0.007 0.001 ARG B 263 *********************** 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 194 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 0.915 Fit side-chains REVERT: A 178 MET cc_start: 0.7920 (mtt) cc_final: 0.6129 (mtt) REVERT: A 202 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6733 (t0) REVERT: A 230 SER cc_start: 0.7215 (m) cc_final: 0.6805 (t) REVERT: B 132 TRP cc_start: 0.8193 (t60) cc_final: 0.7829 (t60) REVERT: C 178 MET cc_start: 0.7853 (mtt) cc_final: 0.6233 (mtt) REVERT: C 230 SER cc_start: 0.7185 (m) cc_final: 0.6781 (t) REVERT: D 132 TRP cc_start: 0.8237 (t60) cc_final: 0.7781 (t60) outliers start: 30 outliers final: 15 residues processed: 184 average time/residue: 0.2099 time to fit residues: 52.2349 Evaluate side-chains 135 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 202 ASP 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 68 LEU 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: 10.0000 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 177 GLN D 184 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8966 Z= 0.219 Angle : 0.599 8.863 12516 Z= 0.337 Chirality : 0.043 0.163 1388 Planarity : 0.004 0.031 1258 Dihedral : 26.484 179.209 1916 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.84 % Allowed : 15.48 % Favored : 81.68 % 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: 0.20 (0.25), residues: 352 sheet: -0.17 (0.35), residues: 220 loop : -1.95 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 61 HIS 0.009 0.001 HIS D 183 PHE 0.013 0.002 PHE A 100 TYR 0.016 0.002 TYR A 99 ARG 0.013 0.001 ARG C 224 *********************** 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 158 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.025 Fit side-chains REVERT: A 178 MET cc_start: 0.8221 (mtt) cc_final: 0.6562 (mtt) REVERT: A 230 SER cc_start: 0.7002 (m) cc_final: 0.6628 (t) REVERT: B 132 TRP cc_start: 0.8322 (t60) cc_final: 0.7830 (t60) REVERT: C 178 MET cc_start: 0.8118 (mtt) cc_final: 0.6438 (mtt) REVERT: C 230 SER cc_start: 0.6966 (m) cc_final: 0.6592 (t) REVERT: D 132 TRP cc_start: 0.8370 (t60) cc_final: 0.7615 (t60) outliers start: 20 outliers final: 14 residues processed: 153 average time/residue: 0.2094 time to fit residues: 44.0645 Evaluate side-chains 127 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU 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 120 ASN 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 225 VAL 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: 3.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 0.0070 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN C 184 ASN D 114 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8966 Z= 0.186 Angle : 0.563 9.827 12516 Z= 0.319 Chirality : 0.041 0.144 1388 Planarity : 0.003 0.026 1258 Dihedral : 26.506 178.952 1916 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.55 % Allowed : 16.62 % Favored : 79.83 % 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: -0.25 (0.29), residues: 822 helix: 0.79 (0.26), residues: 352 sheet: 0.15 (0.35), residues: 220 loop : -1.76 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.005 0.001 HIS D 183 PHE 0.021 0.002 PHE B 100 TYR 0.016 0.001 TYR C 99 ARG 0.008 0.001 ARG C 224 *********************** 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: 25 poor density : 137 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8619 (tt) cc_final: 0.8336 (tt) REVERT: A 178 MET cc_start: 0.8152 (mtt) cc_final: 0.7063 (mtt) REVERT: A 230 SER cc_start: 0.6872 (m) cc_final: 0.6470 (t) REVERT: B 132 TRP cc_start: 0.8354 (t60) cc_final: 0.7876 (t60) REVERT: C 178 MET cc_start: 0.8161 (mtt) cc_final: 0.7062 (mtt) REVERT: C 230 SER cc_start: 0.6852 (m) cc_final: 0.6468 (t) REVERT: D 132 TRP cc_start: 0.8372 (t60) cc_final: 0.7785 (t60) outliers start: 25 outliers final: 17 residues processed: 152 average time/residue: 0.2112 time to fit residues: 43.3311 Evaluate side-chains 130 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 259 VAL Chi-restraints excluded: chain C residue 101 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN C 184 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8966 Z= 0.376 Angle : 0.670 6.974 12516 Z= 0.377 Chirality : 0.045 0.164 1388 Planarity : 0.004 0.032 1258 Dihedral : 27.044 179.819 1916 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.84 % Allowed : 18.04 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.28), residues: 822 helix: 0.55 (0.25), residues: 342 sheet: 0.11 (0.37), residues: 206 loop : -1.79 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 61 HIS 0.009 0.002 HIS B 183 PHE 0.017 0.002 PHE A 121 TYR 0.021 0.003 TYR C 143 ARG 0.007 0.001 ARG C 224 *********************** 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: 27 poor density : 121 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.8314 (mtt) cc_final: 0.7169 (mtt) REVERT: A 269 ARG cc_start: 0.3646 (tpt90) cc_final: 0.3375 (tpt170) REVERT: B 132 TRP cc_start: 0.8541 (t60) cc_final: 0.7746 (t60) REVERT: B 231 ARG cc_start: 0.5936 (mtt90) cc_final: 0.5455 (ttm-80) REVERT: C 178 MET cc_start: 0.8302 (mtt) cc_final: 0.7228 (mtt) REVERT: C 191 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7568 (mm) REVERT: D 132 TRP cc_start: 0.8528 (t60) cc_final: 0.7756 (t60) REVERT: D 178 MET cc_start: 0.6816 (tpp) cc_final: 0.6587 (tpp) outliers start: 27 outliers final: 23 residues processed: 136 average time/residue: 0.1807 time to fit residues: 35.1406 Evaluate side-chains 135 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 112 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 LEU 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 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 172 LEU 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: 0.9980 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.0370 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8966 Z= 0.174 Angle : 0.551 5.691 12516 Z= 0.313 Chirality : 0.041 0.152 1388 Planarity : 0.003 0.028 1258 Dihedral : 26.676 179.480 1916 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.41 % Allowed : 20.60 % Favored : 75.99 % 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: -0.15 (0.29), residues: 822 helix: 0.92 (0.26), residues: 352 sheet: 0.20 (0.37), residues: 216 loop : -1.76 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.004 0.001 HIS C 12 PHE 0.013 0.001 PHE A 181 TYR 0.015 0.002 TYR B 83 ARG 0.005 0.001 ARG C 224 *********************** 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 142 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.894 Fit side-chains REVERT: A 63 LEU cc_start: 0.8657 (tt) cc_final: 0.8356 (tt) REVERT: A 178 MET cc_start: 0.8092 (mtt) cc_final: 0.7846 (mtt) REVERT: A 269 ARG cc_start: 0.3646 (tpt90) cc_final: 0.3444 (tpt170) REVERT: C 18 ASN cc_start: 0.7318 (p0) cc_final: 0.7089 (p0) outliers start: 24 outliers final: 17 residues processed: 130 average time/residue: 0.1840 time to fit residues: 34.5345 Evaluate side-chains 115 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 124 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: 5.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN C 51 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8966 Z= 0.223 Angle : 0.575 5.234 12516 Z= 0.328 Chirality : 0.043 0.214 1388 Planarity : 0.004 0.030 1258 Dihedral : 26.814 179.518 1916 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.84 % Allowed : 20.31 % Favored : 75.85 % 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: -0.10 (0.29), residues: 822 helix: 0.92 (0.26), residues: 350 sheet: 0.17 (0.37), residues: 216 loop : -1.59 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 61 HIS 0.003 0.001 HIS B 183 PHE 0.016 0.001 PHE D 100 TYR 0.016 0.002 TYR D 83 ARG 0.004 0.001 ARG C 224 *********************** 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 125 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.937 Fit side-chains REVERT: C 178 MET cc_start: 0.8135 (mtm) cc_final: 0.7860 (mtt) outliers start: 27 outliers final: 24 residues processed: 117 average time/residue: 0.1600 time to fit residues: 27.9805 Evaluate side-chains 119 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 A residue 203 ILE Chi-restraints excluded: chain B residue 68 LEU 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 112 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 172 LEU 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 C residue 203 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 83 optimal weight: 0.1980 chunk 75 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8966 Z= 0.174 Angle : 0.566 7.653 12516 Z= 0.321 Chirality : 0.042 0.245 1388 Planarity : 0.003 0.028 1258 Dihedral : 26.581 179.604 1916 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.98 % Allowed : 20.45 % Favored : 75.57 % 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: 0.04 (0.30), residues: 822 helix: 0.95 (0.26), residues: 354 sheet: 0.39 (0.39), residues: 202 loop : -1.47 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.004 0.001 HIS C 51 PHE 0.008 0.001 PHE C 100 TYR 0.020 0.002 TYR D 83 ARG 0.004 0.000 ARG C 224 *********************** 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 125 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 0.893 Fit side-chains REVERT: A 178 MET cc_start: 0.8149 (mtm) cc_final: 0.7857 (mtt) REVERT: A 181 PHE cc_start: 0.8218 (t80) cc_final: 0.7998 (t80) REVERT: C 18 ASN cc_start: 0.7499 (p0) cc_final: 0.7278 (p0) REVERT: C 178 MET cc_start: 0.8017 (mtm) cc_final: 0.7789 (mtt) outliers start: 28 outliers final: 25 residues processed: 116 average time/residue: 0.1661 time to fit residues: 28.7881 Evaluate side-chains 114 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 68 LEU 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 112 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 124 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 39 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 184 ASN 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 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: 3.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.6235 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= 0.194 Angle : 0.574 7.331 12516 Z= 0.327 Chirality : 0.042 0.241 1388 Planarity : 0.003 0.029 1258 Dihedral : 26.534 179.083 1916 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.98 % Allowed : 20.60 % Favored : 75.43 % 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: 0.06 (0.29), residues: 822 helix: 1.04 (0.26), residues: 352 sheet: 0.32 (0.39), residues: 202 loop : -1.49 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 132 HIS 0.004 0.001 HIS C 51 PHE 0.017 0.001 PHE D 100 TYR 0.018 0.002 TYR B 83 ARG 0.004 0.000 ARG C 224 *********************** 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: 28 poor density : 91 time to evaluate : 0.826 Fit side-chains REVERT: A 178 MET cc_start: 0.8175 (mtm) cc_final: 0.7877 (mtt) REVERT: A 181 PHE cc_start: 0.8253 (t80) cc_final: 0.7998 (t80) REVERT: C 18 ASN cc_start: 0.7522 (p0) cc_final: 0.7283 (p0) REVERT: D 263 ARG cc_start: 0.6800 (mtm110) cc_final: 0.6559 (mtm110) outliers start: 28 outliers final: 25 residues processed: 112 average time/residue: 0.1629 time to fit residues: 27.1268 Evaluate side-chains 113 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 A residue 203 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 101 LEU 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 104 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: 0.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8966 Z= 0.228 Angle : 0.593 8.810 12516 Z= 0.335 Chirality : 0.043 0.296 1388 Planarity : 0.003 0.029 1258 Dihedral : 26.458 179.204 1916 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.84 % Allowed : 21.02 % Favored : 75.14 % 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: -0.03 (0.29), residues: 822 helix: 0.93 (0.26), residues: 352 sheet: 0.25 (0.39), residues: 202 loop : -1.45 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 132 HIS 0.004 0.001 HIS C 51 PHE 0.029 0.002 PHE B 100 TYR 0.019 0.002 TYR D 83 ARG 0.004 0.000 ARG C 224 ********************** 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 119 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.837 Fit side-chains REVERT: C 18 ASN cc_start: 0.7557 (p0) cc_final: 0.7339 (p0) outliers start: 27 outliers final: 26 residues processed: 112 average time/residue: 0.1589 time to fit residues: 26.7463 Evaluate side-chains 116 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 A residue 203 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 101 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.111853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094042 restraints weight = 21558.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096116 restraints weight = 12543.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097592 restraints weight = 8961.131| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8966 Z= 0.273 Angle : 0.608 5.915 12516 Z= 0.347 Chirality : 0.044 0.257 1388 Planarity : 0.004 0.030 1258 Dihedral : 26.536 179.191 1916 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.84 % Allowed : 21.02 % Favored : 75.14 % 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: 0.77 (0.26), residues: 352 sheet: 0.12 (0.39), residues: 202 loop : -1.48 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.004 0.001 HIS C 78 PHE 0.011 0.001 PHE C 121 TYR 0.019 0.002 TYR D 83 ARG 0.004 0.000 ARG C 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1779.49 seconds wall clock time: 33 minutes 29.79 seconds (2009.79 seconds total)