Starting phenix.real_space_refine on Wed Feb 12 22:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u1c_8481/02_2025/5u1c_8481.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u1c_8481/02_2025/5u1c_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/cci-nas-00/data/ceres_data/5u1c_8481/02_2025/5u1c_8481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u1c_8481/02_2025/5u1c_8481.map" model { file = "/net/cci-nas-00/data/ceres_data/5u1c_8481/02_2025/5u1c_8481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u1c_8481/02_2025/5u1c_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-5592/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: 5.17, 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 - 3.00 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: 2.21 Conformation dependent library (CDL) restraints added in 756.1 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: 3.30 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: 2.98 Time building geometry restraints manager: 2.54 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: 0.04 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'J' } 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 '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: 0.630 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 26.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.390 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 0.816 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: 0.2680 time to fit residues: 93.4840 Evaluate side-chains 134 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096536 restraints weight = 21374.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098579 restraints weight = 12976.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099996 restraints weight = 9572.876| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.826 Fit side-chains REVERT: A 69 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7324 (tt0) REVERT: A 103 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8263 (mtpt) REVERT: A 178 MET cc_start: 0.8794 (mtt) cc_final: 0.6835 (mtt) REVERT: A 230 SER cc_start: 0.7441 (m) cc_final: 0.6979 (t) REVERT: B 65 CYS cc_start: 0.7431 (p) cc_final: 0.7154 (t) REVERT: B 132 TRP cc_start: 0.8796 (t60) cc_final: 0.7915 (t60) REVERT: C 15 TYR cc_start: 0.8727 (m-10) cc_final: 0.8514 (m-10) REVERT: C 20 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8265 (ttm-80) REVERT: C 107 ARG cc_start: 0.7103 (mpp80) cc_final: 0.6852 (mpp80) REVERT: C 178 MET cc_start: 0.8800 (mtt) cc_final: 0.6777 (mtt) REVERT: C 230 SER cc_start: 0.7403 (m) cc_final: 0.6947 (t) REVERT: D 65 CYS cc_start: 0.7442 (p) cc_final: 0.7114 (t) REVERT: D 132 TRP cc_start: 0.8828 (t60) cc_final: 0.7980 (t60) outliers start: 25 outliers final: 14 residues processed: 177 average time/residue: 0.2316 time to fit residues: 54.6862 Evaluate side-chains 132 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LYS 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 80 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098440 restraints weight = 21757.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.100664 restraints weight = 12991.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102125 restraints weight = 9408.588| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8966 Z= 0.198 Angle : 0.596 8.920 12516 Z= 0.335 Chirality : 0.043 0.162 1388 Planarity : 0.004 0.055 1258 Dihedral : 26.411 178.928 1916 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.41 % Allowed : 15.48 % Favored : 82.10 % 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: 0.24 (0.26), residues: 350 sheet: -0.19 (0.35), residues: 210 loop : -1.92 (0.35), residues: 262 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 0.011 0.001 PHE C 100 TYR 0.017 0.002 TYR A 99 ARG 0.006 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 to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.659 Fit side-chains REVERT: A 69 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7183 (tt0) REVERT: A 178 MET cc_start: 0.8854 (mtt) cc_final: 0.6923 (mtt) REVERT: A 184 ASN cc_start: 0.8325 (m-40) cc_final: 0.8083 (m110) REVERT: A 230 SER cc_start: 0.7452 (m) cc_final: 0.6964 (t) REVERT: A 269 ARG cc_start: 0.4739 (tmt170) cc_final: 0.4478 (tpt90) REVERT: B 65 CYS cc_start: 0.7321 (p) cc_final: 0.7057 (t) REVERT: B 132 TRP cc_start: 0.8813 (t60) cc_final: 0.8151 (t60) REVERT: C 20 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.7990 (ttm-80) REVERT: C 144 ASN cc_start: 0.8971 (t0) cc_final: 0.8769 (t0) REVERT: C 178 MET cc_start: 0.8842 (mtt) cc_final: 0.7044 (mtt) REVERT: C 230 SER cc_start: 0.7423 (m) cc_final: 0.6932 (t) REVERT: D 65 CYS cc_start: 0.7348 (p) cc_final: 0.7131 (t) REVERT: D 83 TYR cc_start: 0.7138 (t80) cc_final: 0.6828 (t80) REVERT: D 132 TRP cc_start: 0.8790 (t60) cc_final: 0.7874 (t60) outliers start: 17 outliers final: 12 residues processed: 151 average time/residue: 0.2004 time to fit residues: 41.6437 Evaluate side-chains 128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 89 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 183 HIS C 51 HIS ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN D 114 HIS D 168 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.117853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.099160 restraints weight = 21557.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.101352 restraints weight = 12872.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.102894 restraints weight = 9335.795| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5093 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= 0.176 Angle : 0.564 5.854 12516 Z= 0.321 Chirality : 0.042 0.145 1388 Planarity : 0.004 0.047 1258 Dihedral : 26.465 179.215 1916 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.98 % Allowed : 17.05 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.28), residues: 822 helix: 0.77 (0.27), residues: 350 sheet: 0.09 (0.35), residues: 214 loop : -1.79 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.008 0.001 HIS B 183 PHE 0.027 0.002 PHE D 100 TYR 0.015 0.002 TYR C 99 ARG 0.004 0.001 ARG B 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 161 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.838 Fit side-chains REVERT: A 103 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8320 (ttmt) REVERT: A 144 ASN cc_start: 0.8938 (t0) cc_final: 0.8651 (t0) REVERT: A 178 MET cc_start: 0.8938 (mtt) cc_final: 0.7033 (mtt) REVERT: A 184 ASN cc_start: 0.8390 (m-40) cc_final: 0.8055 (m110) REVERT: A 230 SER cc_start: 0.7363 (m) cc_final: 0.6861 (t) REVERT: A 269 ARG cc_start: 0.4779 (tmt170) cc_final: 0.4475 (tpt90) REVERT: B 132 TRP cc_start: 0.8780 (t60) cc_final: 0.8033 (t60) REVERT: B 229 ASP cc_start: 0.7522 (m-30) cc_final: 0.7267 (m-30) REVERT: C 178 MET cc_start: 0.8899 (mtt) cc_final: 0.7033 (mtt) REVERT: C 230 SER cc_start: 0.7382 (m) cc_final: 0.7106 (t) REVERT: D 96 GLU cc_start: 0.7010 (mp0) cc_final: 0.6738 (mp0) REVERT: D 132 TRP cc_start: 0.8812 (t60) cc_final: 0.7904 (t60) outliers start: 21 outliers final: 14 residues processed: 151 average time/residue: 0.2146 time to fit residues: 44.2472 Evaluate side-chains 136 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 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 57 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 83 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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** B 114 HIS C 184 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.115247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096561 restraints weight = 21717.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098654 restraints weight = 13408.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100074 restraints weight = 9879.493| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8966 Z= 0.231 Angle : 0.590 6.871 12516 Z= 0.335 Chirality : 0.043 0.201 1388 Planarity : 0.004 0.032 1258 Dihedral : 26.687 179.871 1916 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.70 % Allowed : 19.32 % Favored : 77.98 % 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: -0.19 (0.28), residues: 822 helix: 0.87 (0.26), residues: 352 sheet: 0.12 (0.36), residues: 214 loop : -1.67 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 132 HIS 0.004 0.001 HIS C 51 PHE 0.019 0.002 PHE B 100 TYR 0.012 0.002 TYR A 143 ARG 0.005 0.000 ARG C 20 *********************** 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 to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASN cc_start: 0.8909 (t0) cc_final: 0.8641 (t0) REVERT: A 178 MET cc_start: 0.8941 (mtt) cc_final: 0.8280 (mtt) REVERT: A 184 ASN cc_start: 0.8475 (m-40) cc_final: 0.8262 (m110) REVERT: A 194 TYR cc_start: 0.7800 (m-80) cc_final: 0.7504 (m-80) REVERT: C 178 MET cc_start: 0.8983 (mtt) cc_final: 0.8313 (mtt) REVERT: D 83 TYR cc_start: 0.7751 (t80) cc_final: 0.7105 (t80) REVERT: D 85 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7335 (mt-10) REVERT: D 96 GLU cc_start: 0.7058 (mp0) cc_final: 0.6670 (mp0) outliers start: 19 outliers final: 18 residues processed: 141 average time/residue: 0.1994 time to fit residues: 39.4776 Evaluate side-chains 133 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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 112 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** B 114 HIS C 184 ASN D 114 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.115064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096351 restraints weight = 21165.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098614 restraints weight = 12149.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100124 restraints weight = 8649.910| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5769 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= 0.221 Angle : 0.588 7.817 12516 Z= 0.333 Chirality : 0.043 0.239 1388 Planarity : 0.004 0.052 1258 Dihedral : 26.706 179.959 1916 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.84 % Allowed : 19.60 % Favored : 76.56 % 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: -0.05 (0.29), residues: 822 helix: 0.96 (0.27), residues: 350 sheet: 0.09 (0.36), residues: 214 loop : -1.44 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.004 0.001 HIS C 12 PHE 0.010 0.001 PHE C 121 TYR 0.014 0.002 TYR A 143 ARG 0.005 0.001 ARG A 269 *********************** 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 147 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.819 Fit side-chains REVERT: A 144 ASN cc_start: 0.8992 (t0) cc_final: 0.8618 (t0) REVERT: A 178 MET cc_start: 0.9047 (mtt) cc_final: 0.8310 (mtt) REVERT: A 184 ASN cc_start: 0.8451 (m-40) cc_final: 0.8221 (m110) REVERT: A 269 ARG cc_start: 0.4663 (tpt90) cc_final: 0.4332 (tpt170) REVERT: B 74 LEU cc_start: 0.8839 (mp) cc_final: 0.8342 (tp) REVERT: B 100 PHE cc_start: 0.8430 (t80) cc_final: 0.8222 (t80) REVERT: B 232 ASP cc_start: 0.8369 (t0) cc_final: 0.8076 (m-30) REVERT: C 178 MET cc_start: 0.9086 (mtt) cc_final: 0.8843 (mtm) REVERT: C 191 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7696 (mm) REVERT: D 83 TYR cc_start: 0.7787 (t80) cc_final: 0.6914 (t80) REVERT: D 85 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6535 (mt-10) REVERT: D 87 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7192 (tm-30) REVERT: D 178 MET cc_start: 0.7871 (tpp) cc_final: 0.7654 (tpp) outliers start: 27 outliers final: 18 residues processed: 137 average time/residue: 0.2043 time to fit residues: 38.6280 Evaluate side-chains 130 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain C residue 107 ARG 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 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 77 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 164 GLN ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098801 restraints weight = 21652.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.100919 restraints weight = 13151.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102388 restraints weight = 9610.353| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5988 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= 0.183 Angle : 0.578 8.988 12516 Z= 0.325 Chirality : 0.042 0.251 1388 Planarity : 0.004 0.044 1258 Dihedral : 26.602 179.502 1916 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.12 % Allowed : 21.02 % 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: 0.08 (0.29), residues: 822 helix: 1.04 (0.27), residues: 352 sheet: 0.31 (0.37), residues: 210 loop : -1.49 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.004 0.001 HIS A 51 PHE 0.016 0.001 PHE A 181 TYR 0.014 0.001 TYR B 83 ARG 0.005 0.001 ARG B 199 *********************** 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 141 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.916 Fit side-chains REVERT: A 18 ASN cc_start: 0.7922 (p0) cc_final: 0.7602 (p0) REVERT: A 144 ASN cc_start: 0.8897 (t0) cc_final: 0.8506 (t0) REVERT: A 178 MET cc_start: 0.8904 (mtt) cc_final: 0.8303 (mtm) REVERT: A 184 ASN cc_start: 0.8241 (m-40) cc_final: 0.7965 (m110) REVERT: B 232 ASP cc_start: 0.8249 (t0) cc_final: 0.8024 (m-30) REVERT: C 178 MET cc_start: 0.8971 (mtt) cc_final: 0.8362 (mtm) REVERT: D 83 TYR cc_start: 0.7711 (t80) cc_final: 0.7023 (t80) outliers start: 22 outliers final: 17 residues processed: 130 average time/residue: 0.1817 time to fit residues: 33.9876 Evaluate side-chains 125 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 89 ILE 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 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 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 33 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** C 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.116877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099018 restraints weight = 21891.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101075 restraints weight = 13032.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.102544 restraints weight = 9410.767| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8966 Z= 0.189 Angle : 0.580 10.906 12516 Z= 0.326 Chirality : 0.042 0.183 1388 Planarity : 0.004 0.034 1258 Dihedral : 26.600 178.914 1916 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.70 % Allowed : 21.73 % 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: 0.12 (0.29), residues: 822 helix: 1.07 (0.27), residues: 352 sheet: 0.38 (0.37), residues: 210 loop : -1.50 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.004 0.001 HIS D 183 PHE 0.008 0.001 PHE A 121 TYR 0.019 0.001 TYR B 83 ARG 0.006 0.001 ARG C 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 129 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.844 Fit side-chains REVERT: A 18 ASN cc_start: 0.7966 (p0) cc_final: 0.7629 (p0) REVERT: A 144 ASN cc_start: 0.8880 (t0) cc_final: 0.8439 (t0) REVERT: A 178 MET cc_start: 0.8939 (mtt) cc_final: 0.8326 (mtm) REVERT: A 184 ASN cc_start: 0.8239 (m-40) cc_final: 0.7934 (m110) REVERT: B 83 TYR cc_start: 0.7520 (t80) cc_final: 0.7060 (t80) REVERT: B 232 ASP cc_start: 0.8298 (t0) cc_final: 0.8022 (m-30) REVERT: C 178 MET cc_start: 0.8994 (mtt) cc_final: 0.8355 (mtm) REVERT: D 74 LEU cc_start: 0.8454 (tp) cc_final: 0.8200 (mp) outliers start: 19 outliers final: 16 residues processed: 121 average time/residue: 0.1695 time to fit residues: 30.2748 Evaluate side-chains 123 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 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 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 41 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.096652 restraints weight = 21779.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098807 restraints weight = 12995.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.100235 restraints weight = 9406.559| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8966 Z= 0.219 Angle : 0.600 9.317 12516 Z= 0.336 Chirality : 0.043 0.201 1388 Planarity : 0.004 0.034 1258 Dihedral : 26.480 179.172 1916 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.84 % Allowed : 21.88 % Favored : 75.28 % 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: 1.02 (0.27), residues: 352 sheet: 0.40 (0.38), residues: 206 loop : -1.56 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 61 HIS 0.005 0.001 HIS D 183 PHE 0.022 0.001 PHE B 100 TYR 0.021 0.002 TYR B 83 ARG 0.004 0.001 ARG C 107 *********************** 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 130 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.951 Fit side-chains REVERT: A 144 ASN cc_start: 0.8880 (t0) cc_final: 0.8434 (t0) REVERT: A 178 MET cc_start: 0.8957 (mtt) cc_final: 0.8354 (mtm) REVERT: A 184 ASN cc_start: 0.8418 (m-40) cc_final: 0.8161 (m110) REVERT: B 232 ASP cc_start: 0.8281 (t0) cc_final: 0.8048 (m-30) REVERT: C 178 MET cc_start: 0.8985 (mtt) cc_final: 0.8630 (mtt) REVERT: D 74 LEU cc_start: 0.8483 (tp) cc_final: 0.8213 (mp) REVERT: D 83 TYR cc_start: 0.7684 (t80) cc_final: 0.7174 (t80) REVERT: D 85 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7801 (mm-30) REVERT: D 178 MET cc_start: 0.7963 (tpp) cc_final: 0.7571 (tpp) REVERT: D 232 ASP cc_start: 0.8327 (t0) cc_final: 0.8063 (m-30) outliers start: 20 outliers final: 18 residues processed: 123 average time/residue: 0.1608 time to fit residues: 29.4277 Evaluate side-chains 121 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 89 ILE 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 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 112 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.0060 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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** C 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.117638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.099362 restraints weight = 21403.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101649 restraints weight = 12135.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103165 restraints weight = 8483.030| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6384 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= 0.180 Angle : 0.591 9.221 12516 Z= 0.330 Chirality : 0.042 0.225 1388 Planarity : 0.004 0.034 1258 Dihedral : 26.264 179.221 1916 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.98 % Allowed : 21.73 % Favored : 75.28 % 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: 0.17 (0.29), residues: 822 helix: 1.11 (0.27), residues: 354 sheet: 0.45 (0.38), residues: 206 loop : -1.53 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 132 HIS 0.004 0.001 HIS A 51 PHE 0.007 0.001 PHE A 121 TYR 0.016 0.001 TYR B 83 ARG 0.004 0.001 ARG B 199 ********************** 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 127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.920 Fit side-chains REVERT: A 18 ASN cc_start: 0.8179 (p0) cc_final: 0.7473 (p0) REVERT: A 66 THR cc_start: 0.9416 (t) cc_final: 0.9081 (m) REVERT: A 144 ASN cc_start: 0.8968 (t0) cc_final: 0.8438 (t0) REVERT: A 178 MET cc_start: 0.9040 (mtt) cc_final: 0.8654 (mtt) REVERT: A 184 ASN cc_start: 0.8266 (m-40) cc_final: 0.7906 (m110) REVERT: B 232 ASP cc_start: 0.8382 (t0) cc_final: 0.7997 (m-30) REVERT: C 18 ASN cc_start: 0.7964 (p0) cc_final: 0.7736 (p0) REVERT: C 178 MET cc_start: 0.9053 (mtt) cc_final: 0.8667 (mtt) REVERT: C 194 TYR cc_start: 0.7792 (m-80) cc_final: 0.7472 (m-80) outliers start: 21 outliers final: 16 residues processed: 118 average time/residue: 0.1753 time to fit residues: 30.8675 Evaluate side-chains 116 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 89 ILE 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 102 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 184 ASN 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 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 37 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** ** D 164 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 = 0.3788 r_free = 0.3788 target = 0.117734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.100139 restraints weight = 21426.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.102184 restraints weight = 12710.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.103577 restraints weight = 9175.685| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 8966 Z= 0.340 Angle : 0.930 59.199 12516 Z= 0.552 Chirality : 0.048 0.581 1388 Planarity : 0.004 0.034 1258 Dihedral : 26.278 179.200 1916 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.92 % Favored : 96.96 % Rotamer: Outliers : 2.41 % Allowed : 22.59 % Favored : 75.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.14 (0.29), residues: 822 helix: 1.08 (0.27), residues: 354 sheet: 0.45 (0.38), residues: 206 loop : -1.53 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 132 HIS 0.010 0.001 HIS C 183 PHE 0.009 0.001 PHE C 181 TYR 0.013 0.001 TYR B 83 ARG 0.008 0.001 ARG C 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.16 seconds wall clock time: 43 minutes 23.43 seconds (2603.43 seconds total)