Starting phenix.real_space_refine on Fri Jul 3 05:07:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oos_17027/07_2026/8oos_17027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oos_17027/07_2026/8oos_17027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oos_17027/07_2026/8oos_17027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oos_17027/07_2026/8oos_17027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oos_17027/07_2026/8oos_17027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oos_17027/07_2026/8oos_17027.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oos_17027/07_2026/8oos_17027.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oos_17027/07_2026/8oos_17027.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.026 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 219 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 7085 2.51 5 N 2272 2.21 5 O 2689 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12307 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3622 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 425} Chain breaks: 3 Chain: "K" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2243 Classifications: {'DNA': 110} Link IDs: {'rna3p': 109} Chain: "L" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 2201 Classifications: {'DNA': 107} Link IDs: {'rna3p': 106} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 602 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "P" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "R" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.59, per 1000 atoms: 0.21 Number of scatterers: 12307 At special positions: 0 Unit cell: (117.546, 144.672, 108.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 36 16.00 P 219 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2689 8.00 N 2272 7.00 C 7085 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 278.8 milliseconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 64.7% alpha, 5.5% beta 67 base pairs and 187 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'G' and resid 965 through 969 Processing helix chain 'G' and resid 973 through 989 Processing helix chain 'G' and resid 1002 through 1019 removed outlier: 3.688A pdb=" N ILE G1008 " --> pdb=" O THR G1004 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET G1011 " --> pdb=" O SER G1007 " (cutoff:3.500A) Processing helix chain 'G' and resid 1029 through 1031 No H-bonds generated for 'chain 'G' and resid 1029 through 1031' Processing helix chain 'G' and resid 1032 through 1044 Processing helix chain 'G' and resid 1055 through 1063 Processing helix chain 'G' and resid 1064 through 1066 No H-bonds generated for 'chain 'G' and resid 1064 through 1066' Processing helix chain 'G' and resid 1087 through 1092 Processing helix chain 'G' and resid 1092 through 1097 Processing helix chain 'G' and resid 1108 through 1113 Processing helix chain 'G' and resid 1117 through 1124 removed outlier: 3.684A pdb=" N LEU G1123 " --> pdb=" O ARG G1119 " (cutoff:3.500A) Processing helix chain 'G' and resid 1143 through 1154 removed outlier: 4.345A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1189 through 1193 Processing helix chain 'G' and resid 1223 through 1240 removed outlier: 4.011A pdb=" N GLN G1236 " --> pdb=" O SER G1232 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE G1237 " --> pdb=" O LEU G1233 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1270 removed outlier: 4.968A pdb=" N MET G1262 " --> pdb=" O MET G1258 " (cutoff:3.500A) Processing helix chain 'G' and resid 1271 through 1274 Processing helix chain 'G' and resid 1544 through 1551 Processing helix chain 'G' and resid 1552 through 1569 Processing helix chain 'G' and resid 1579 through 1591 Processing helix chain 'G' and resid 1604 through 1618 Processing helix chain 'G' and resid 1651 through 1663 removed outlier: 4.062A pdb=" N ASP G1655 " --> pdb=" O ASN G1651 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA G1662 " --> pdb=" O ALA G1658 " (cutoff:3.500A) Processing helix chain 'G' and resid 1681 through 1701 removed outlier: 4.264A pdb=" N ARG G1685 " --> pdb=" O THR G1681 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.509A pdb=" N MET M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.512A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.636A pdb=" N ILE N 29 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.505A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG N 55 " --> pdb=" O TYR N 51 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL N 60 " --> pdb=" O GLY N 56 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA N 76 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 46 through 73 Processing helix chain 'O' and resid 79 through 90 Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 34 through 46 removed outlier: 3.849A pdb=" N GLN P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 82 Processing helix chain 'P' and resid 87 through 99 Processing helix chain 'P' and resid 100 through 119 Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 63 through 77 Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.695A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.555A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.610A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 removed outlier: 3.585A pdb=" N VAL R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 1049 through 1051 removed outlier: 6.336A pdb=" N MET G1104 " --> pdb=" O LEU G1132 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU G1134 " --> pdb=" O MET G1104 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU G1106 " --> pdb=" O LEU G1134 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY G 993 " --> pdb=" O ARG G1131 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE G 994 " --> pdb=" O LEU G1199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 1214 through 1217 removed outlier: 6.580A pdb=" N ILE G1214 " --> pdb=" O VAL G1673 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG G1675 " --> pdb=" O ILE G1214 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE G1216 " --> pdb=" O ARG G1675 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL G1643 " --> pdb=" O TYR G1674 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU G1573 " --> pdb=" O ILE G1644 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL G1572 " --> pdb=" O PHE G1624 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU G1626 " --> pdb=" O VAL G1572 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU G1574 " --> pdb=" O LEU G1626 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS G1597 " --> pdb=" O LEU G1625 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N SER G1627 " --> pdb=" O CYS G1597 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU G1599 " --> pdb=" O SER G1627 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.699A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.062A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'O' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'Q' and resid 118 through 119 435 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 169 hydrogen bonds 338 hydrogen bond angles 0 basepair planarities 67 basepair parallelities 187 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3106 1.34 - 1.45: 3293 1.45 - 1.57: 6077 1.57 - 1.69: 430 1.69 - 1.81: 66 Bond restraints: 12972 Sorted by residual: bond pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.684 1.801 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.685 1.786 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" F4 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.686 1.785 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.685 1.775 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C3' DC K 21 " pdb=" C2' DC K 21 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.59e+01 ... (remaining 12967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.16: 18426 14.16 - 28.31: 4 28.31 - 42.47: 0 42.47 - 56.62: 0 56.62 - 70.78: 2 Bond angle restraints: 18432 Sorted by residual: angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F2 ALF G2003 " ideal model delta sigma weight residual 108.68 179.46 -70.78 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 109.63 179.87 -70.24 3.00e+00 1.11e-01 5.48e+02 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 110.21 89.83 20.38 3.00e+00 1.11e-01 4.62e+01 angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F3 ALF G2003 " ideal model delta sigma weight residual 109.69 89.55 20.14 3.00e+00 1.11e-01 4.51e+01 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F3 ALF G2003 " ideal model delta sigma weight residual 109.59 90.24 19.35 3.00e+00 1.11e-01 4.16e+01 ... (remaining 18427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 6155 33.00 - 66.00: 1045 66.00 - 98.99: 44 98.99 - 131.99: 2 131.99 - 164.99: 1 Dihedral angle restraints: 7247 sinusoidal: 4430 harmonic: 2817 Sorted by residual: dihedral pdb=" O1B ADP G2001 " pdb=" O3A ADP G2001 " pdb=" PB ADP G2001 " pdb=" PA ADP G2001 " ideal model delta sinusoidal sigma weight residual 300.00 135.01 164.99 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP G2001 " pdb=" O5' ADP G2001 " pdb=" PA ADP G2001 " pdb=" O2A ADP G2001 " ideal model delta sinusoidal sigma weight residual 300.00 177.09 122.92 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" O2A ADP G2001 " pdb=" O3A ADP G2001 " pdb=" PA ADP G2001 " pdb=" PB ADP G2001 " ideal model delta sinusoidal sigma weight residual -60.00 57.31 -117.31 1 2.00e+01 2.50e-03 3.50e+01 ... (remaining 7244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1303 0.050 - 0.100: 665 0.100 - 0.150: 102 0.150 - 0.200: 7 0.200 - 0.250: 1 Chirality restraints: 2078 Sorted by residual: chirality pdb=" CB ILE O 79 " pdb=" CA ILE O 79 " pdb=" CG1 ILE O 79 " pdb=" CG2 ILE O 79 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE O 79 " pdb=" N ILE O 79 " pdb=" C ILE O 79 " pdb=" CB ILE O 79 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" C1' DG K 25 " pdb=" O4' DG K 25 " pdb=" C2' DG K 25 " pdb=" N9 DG K 25 " both_signs ideal model delta sigma weight residual False 2.43 2.24 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2075 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G1086 " 0.000 2.00e-02 2.50e+03 3.58e-02 2.56e+01 pdb=" CG TYR G1086 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR G1086 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR G1086 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR G1086 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR G1086 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G1086 " -0.051 2.00e-02 2.50e+03 pdb=" OH TYR G1086 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 41 " 0.006 2.00e-02 2.50e+03 3.01e-02 1.82e+01 pdb=" CG TYR Q 41 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 41 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 41 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 41 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 41 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR Q 41 " -0.041 2.00e-02 2.50e+03 pdb=" OH TYR Q 41 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G1592 " 0.278 9.50e-02 1.11e+02 1.25e-01 1.20e+01 pdb=" NE ARG G1592 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG G1592 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG G1592 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG G1592 " 0.001 2.00e-02 2.50e+03 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 34 2.48 - 3.09: 8143 3.09 - 3.69: 19964 3.69 - 4.30: 31570 4.30 - 4.90: 47238 Nonbonded interactions: 106949 Sorted by model distance: nonbonded pdb="MG MG G2002 " pdb=" F3 ALF G2003 " model vdw 1.879 2.120 nonbonded pdb=" O2B ADP G2001 " pdb="MG MG G2002 " model vdw 2.019 2.170 nonbonded pdb=" OE2 GLU Q 73 " pdb=" ND2 ASN R 25 " model vdw 2.134 3.120 nonbonded pdb=" OD1 ASP G1559 " pdb=" OH TYR G1588 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR M 99 " pdb=" OE1 GLU M 133 " model vdw 2.228 3.040 ... (remaining 106944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'N' and resid 23 through 93) selection = (chain 'R' and resid 23 through 93) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.007 0.330 12973 Z= 0.592 Angle : 1.284 70.779 18432 Z= 0.663 Chirality : 0.053 0.250 2078 Planarity : 0.012 0.125 1571 Dihedral : 24.793 164.988 5423 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.24), residues: 946 helix: -2.01 (0.17), residues: 578 sheet: 0.33 (0.85), residues: 45 loop : -0.58 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.004 ARG G1592 TYR 0.052 0.007 TYR G1086 PHE 0.018 0.002 PHE G1096 TRP 0.017 0.002 TRP G1650 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.52 (12972) covalent geometry : angle 1.28359 / 0.66 (18432) hydrogen bonds : bond 0.22571 / 14.71 ( 604) hydrogen bonds : angle 8.28872 / 5.92 ( 1598) Misc. bond : bond 0.32952 / 17.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: G 1258 MET cc_start: 0.4246 (mmm) cc_final: 0.3189 (ptm) REVERT: G 1262 MET cc_start: 0.5481 (tpp) cc_final: 0.5180 (tpt) REVERT: G 1585 MET cc_start: 0.7331 (tpt) cc_final: 0.7020 (tpp) REVERT: G 1661 ARG cc_start: 0.4688 (mtp180) cc_final: 0.4473 (mtp85) REVERT: M 129 ARG cc_start: 0.7293 (tpt-90) cc_final: 0.7036 (tpt90) REVERT: O 38 ASN cc_start: 0.7476 (t0) cc_final: 0.7146 (t0) REVERT: O 94 ASN cc_start: 0.7548 (t0) cc_final: 0.7272 (t0) REVERT: O 99 ARG cc_start: 0.7462 (mmt-90) cc_final: 0.6811 (mtp85) REVERT: P 40 LYS cc_start: 0.7836 (mttt) cc_final: 0.7421 (mmtp) REVERT: P 65 ASP cc_start: 0.7484 (t70) cc_final: 0.7089 (t0) REVERT: R 77 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7379 (mttt) REVERT: R 95 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7452 (mtp85) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1534 time to fit residues: 43.1447 Evaluate side-chains 153 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1087 GLN G1186 GLN M 68 GLN P 60 ASN P 81 ASN Q 113 HIS R 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114257 restraints weight = 17494.983| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 0.96 r_work: 0.3410 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12973 Z= 0.220 Angle : 0.964 31.344 18432 Z= 0.478 Chirality : 0.055 0.247 2078 Planarity : 0.006 0.048 1571 Dihedral : 29.519 138.046 3441 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.43 % Allowed : 7.15 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.26), residues: 946 helix: -0.27 (0.20), residues: 589 sheet: 0.74 (0.86), residues: 42 loop : -0.27 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G1201 TYR 0.023 0.003 TYR O 50 PHE 0.021 0.002 PHE G1079 TRP 0.020 0.003 TRP G1650 HIS 0.006 0.002 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (12972) covalent geometry : angle 0.96423 / 0.48 (18432) hydrogen bonds : bond 0.06194 / 3.96 ( 604) hydrogen bonds : angle 4.45945 / 3.23 ( 1598) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1230 TYR cc_start: 0.4739 (t80) cc_final: 0.3991 (t80) REVERT: G 1240 MET cc_start: 0.1410 (OUTLIER) cc_final: 0.0906 (ppp) REVERT: G 1264 PHE cc_start: 0.6189 (m-80) cc_final: 0.5856 (m-80) REVERT: O 38 ASN cc_start: 0.7638 (t0) cc_final: 0.7422 (t0) REVERT: P 117 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7810 (ttmm) REVERT: R 57 VAL cc_start: 0.8097 (t) cc_final: 0.7738 (m) REVERT: R 77 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7428 (mttt) outliers start: 12 outliers final: 8 residues processed: 157 average time/residue: 0.1757 time to fit residues: 35.6385 Evaluate side-chains 141 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1075 LYS Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain R residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 111 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1577 GLN P 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116579 restraints weight = 17672.805| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.01 r_work: 0.3424 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12973 Z= 0.174 Angle : 0.847 31.595 18432 Z= 0.418 Chirality : 0.048 0.250 2078 Planarity : 0.005 0.040 1571 Dihedral : 29.680 132.341 3441 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.91 % Allowed : 9.30 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 946 helix: 0.28 (0.20), residues: 593 sheet: 0.65 (0.86), residues: 42 loop : -0.22 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G1265 TYR 0.025 0.002 TYR N 88 PHE 0.014 0.002 PHE G1079 TRP 0.013 0.002 TRP G1650 HIS 0.008 0.001 HIS P 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (12972) covalent geometry : angle 0.84702 / 0.42 (18432) hydrogen bonds : bond 0.05275 / 3.33 ( 604) hydrogen bonds : angle 4.06280 / 2.93 ( 1598) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: G 1563 ARG cc_start: 0.7127 (mtt90) cc_final: 0.6749 (mtt90) REVERT: G 1650 TRP cc_start: 0.5712 (OUTLIER) cc_final: 0.5508 (t60) REVERT: O 38 ASN cc_start: 0.7764 (t0) cc_final: 0.7515 (t0) REVERT: P 56 MET cc_start: 0.7178 (tpp) cc_final: 0.6869 (mmm) REVERT: P 117 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7771 (ttmm) REVERT: R 57 VAL cc_start: 0.8051 (t) cc_final: 0.7736 (m) REVERT: R 77 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7452 (mttt) outliers start: 16 outliers final: 9 residues processed: 146 average time/residue: 0.1605 time to fit residues: 31.0668 Evaluate side-chains 139 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1075 LYS Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1585 MET Chi-restraints excluded: chain G residue 1650 TRP Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 101 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117230 restraints weight = 17605.362| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.00 r_work: 0.3444 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12973 Z= 0.147 Angle : 0.814 30.954 18432 Z= 0.397 Chirality : 0.046 0.252 2078 Planarity : 0.005 0.040 1571 Dihedral : 29.499 130.674 3441 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.03 % Allowed : 11.68 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.27), residues: 946 helix: 0.72 (0.21), residues: 593 sheet: 0.26 (0.83), residues: 47 loop : -0.09 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G1664 TYR 0.015 0.002 TYR P 80 PHE 0.012 0.001 PHE M 67 TRP 0.013 0.002 TRP G1021 HIS 0.007 0.001 HIS G1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (12972) covalent geometry : angle 0.81365 / 0.40 (18432) hydrogen bonds : bond 0.04395 / 2.76 ( 604) hydrogen bonds : angle 3.87240 / 2.80 ( 1598) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: G 1230 TYR cc_start: 0.4750 (t80) cc_final: 0.3922 (t80) REVERT: G 1264 PHE cc_start: 0.6481 (m-80) cc_final: 0.6168 (m-80) REVERT: G 1563 ARG cc_start: 0.7103 (mtt90) cc_final: 0.6898 (mtt90) REVERT: G 1650 TRP cc_start: 0.5709 (OUTLIER) cc_final: 0.5450 (t60) REVERT: N 25 ASN cc_start: 0.7119 (m-40) cc_final: 0.6720 (m110) REVERT: O 38 ASN cc_start: 0.7710 (t0) cc_final: 0.7487 (t0) REVERT: P 56 MET cc_start: 0.7149 (tpp) cc_final: 0.6841 (mmm) REVERT: P 117 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7763 (tttm) REVERT: R 57 VAL cc_start: 0.8025 (t) cc_final: 0.7747 (m) REVERT: R 77 LYS cc_start: 0.7796 (mtmt) cc_final: 0.7537 (mttt) REVERT: R 78 ARG cc_start: 0.6177 (ttp-110) cc_final: 0.5733 (mtm-85) outliers start: 17 outliers final: 6 residues processed: 146 average time/residue: 0.1690 time to fit residues: 32.7910 Evaluate side-chains 130 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain G residue 1650 TRP Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain Q residue 117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 84 optimal weight: 0.0870 chunk 109 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116821 restraints weight = 17621.338| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.00 r_work: 0.3439 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12973 Z= 0.149 Angle : 0.806 30.947 18432 Z= 0.392 Chirality : 0.045 0.260 2078 Planarity : 0.004 0.037 1571 Dihedral : 29.429 127.367 3441 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.79 % Allowed : 13.35 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 946 helix: 0.86 (0.21), residues: 592 sheet: 0.16 (0.82), residues: 47 loop : -0.07 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 42 TYR 0.026 0.002 TYR N 88 PHE 0.012 0.001 PHE M 67 TRP 0.013 0.002 TRP G1650 HIS 0.007 0.001 HIS G1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (12972) covalent geometry : angle 0.80637 / 0.39 (18432) hydrogen bonds : bond 0.04357 / 2.73 ( 604) hydrogen bonds : angle 3.83840 / 2.78 ( 1598) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6459 (m-80) cc_final: 0.6027 (m-80) REVERT: G 1563 ARG cc_start: 0.7127 (mtt90) cc_final: 0.6904 (mtt90) REVERT: G 1650 TRP cc_start: 0.5698 (OUTLIER) cc_final: 0.5474 (t60) REVERT: O 38 ASN cc_start: 0.7771 (t0) cc_final: 0.7544 (t0) REVERT: P 56 MET cc_start: 0.7080 (tpp) cc_final: 0.6800 (mmm) REVERT: R 57 VAL cc_start: 0.8082 (t) cc_final: 0.7800 (m) REVERT: R 77 LYS cc_start: 0.7816 (mtmt) cc_final: 0.7496 (mttt) outliers start: 15 outliers final: 9 residues processed: 137 average time/residue: 0.1388 time to fit residues: 25.5757 Evaluate side-chains 130 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1585 MET Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain G residue 1650 TRP Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116458 restraints weight = 17551.896| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.00 r_work: 0.3436 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12973 Z= 0.153 Angle : 0.810 31.068 18432 Z= 0.392 Chirality : 0.045 0.254 2078 Planarity : 0.004 0.037 1571 Dihedral : 29.382 125.508 3441 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.26 % Allowed : 13.95 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.27), residues: 946 helix: 0.90 (0.21), residues: 593 sheet: 0.22 (0.82), residues: 47 loop : -0.06 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1664 TYR 0.015 0.002 TYR G1230 PHE 0.012 0.002 PHE Q 67 TRP 0.013 0.002 TRP G1650 HIS 0.006 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (12972) covalent geometry : angle 0.80969 / 0.39 (18432) hydrogen bonds : bond 0.04270 / 2.69 ( 604) hydrogen bonds : angle 3.82567 / 2.76 ( 1598) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6487 (m-80) cc_final: 0.6107 (m-80) REVERT: G 1563 ARG cc_start: 0.7119 (mtt90) cc_final: 0.6871 (mtt90) REVERT: G 1585 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7103 (mmm) REVERT: O 38 ASN cc_start: 0.7741 (t0) cc_final: 0.7523 (t0) REVERT: O 104 GLN cc_start: 0.8143 (mt0) cc_final: 0.7933 (mt0) REVERT: P 56 MET cc_start: 0.7133 (tpp) cc_final: 0.6814 (mmm) REVERT: R 57 VAL cc_start: 0.8065 (t) cc_final: 0.7789 (m) REVERT: R 77 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7515 (mttt) outliers start: 19 outliers final: 13 residues processed: 136 average time/residue: 0.1350 time to fit residues: 24.9257 Evaluate side-chains 133 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1585 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 25 ASN Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116024 restraints weight = 17522.738| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.00 r_work: 0.3430 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12973 Z= 0.156 Angle : 0.814 31.278 18432 Z= 0.392 Chirality : 0.045 0.233 2078 Planarity : 0.004 0.038 1571 Dihedral : 29.340 123.575 3441 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.62 % Allowed : 14.06 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 946 helix: 0.86 (0.21), residues: 600 sheet: 0.31 (0.83), residues: 47 loop : -0.13 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G1017 TYR 0.014 0.002 TYR O 50 PHE 0.013 0.002 PHE G1079 TRP 0.017 0.002 TRP G1650 HIS 0.005 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (12972) covalent geometry : angle 0.81443 / 0.39 (18432) hydrogen bonds : bond 0.04314 / 2.72 ( 604) hydrogen bonds : angle 3.81904 / 2.74 ( 1598) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6604 (m-80) cc_final: 0.6183 (m-80) REVERT: G 1563 ARG cc_start: 0.7205 (mtt90) cc_final: 0.6862 (mtt90) REVERT: G 1585 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7114 (mmm) REVERT: O 38 ASN cc_start: 0.7754 (t0) cc_final: 0.7518 (t0) REVERT: R 57 VAL cc_start: 0.8064 (t) cc_final: 0.7789 (m) REVERT: R 77 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7522 (mttt) outliers start: 22 outliers final: 17 residues processed: 141 average time/residue: 0.1381 time to fit residues: 26.6682 Evaluate side-chains 138 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1585 MET Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 25 ASN Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.0030 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 0.0070 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1141 ASN G1207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118071 restraints weight = 17495.792| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.00 r_work: 0.3458 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 12973 Z= 0.130 Angle : 0.788 30.541 18432 Z= 0.380 Chirality : 0.044 0.254 2078 Planarity : 0.004 0.037 1571 Dihedral : 29.171 123.630 3441 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.55 % Allowed : 16.09 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.27), residues: 946 helix: 1.05 (0.21), residues: 600 sheet: 0.43 (0.84), residues: 47 loop : -0.10 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 78 TYR 0.054 0.002 TYR P 80 PHE 0.012 0.001 PHE M 67 TRP 0.017 0.002 TRP G1650 HIS 0.003 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (12972) covalent geometry : angle 0.78789 / 0.38 (18432) hydrogen bonds : bond 0.03905 / 2.45 ( 604) hydrogen bonds : angle 3.79315 / 2.74 ( 1598) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6540 (m-80) cc_final: 0.6139 (m-80) REVERT: G 1563 ARG cc_start: 0.7171 (mtt90) cc_final: 0.6928 (mtt90) REVERT: G 1585 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.7043 (mmm) REVERT: O 38 ASN cc_start: 0.7737 (t0) cc_final: 0.7498 (t0) REVERT: P 56 MET cc_start: 0.7162 (tpp) cc_final: 0.6938 (mmm) REVERT: R 57 VAL cc_start: 0.8050 (t) cc_final: 0.7783 (m) REVERT: R 77 LYS cc_start: 0.7833 (mtmt) cc_final: 0.7546 (mttt) outliers start: 13 outliers final: 11 residues processed: 137 average time/residue: 0.1310 time to fit residues: 24.4777 Evaluate side-chains 135 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1585 MET Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 25 ASN Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115107 restraints weight = 17717.711| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 0.99 r_work: 0.3413 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12973 Z= 0.188 Angle : 0.844 31.479 18432 Z= 0.408 Chirality : 0.047 0.236 2078 Planarity : 0.005 0.042 1571 Dihedral : 29.343 120.720 3441 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.38 % Allowed : 15.97 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.27), residues: 946 helix: 0.68 (0.21), residues: 601 sheet: 0.19 (0.82), residues: 47 loop : -0.32 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 78 TYR 0.057 0.003 TYR P 80 PHE 0.020 0.002 PHE G1079 TRP 0.015 0.002 TRP G1650 HIS 0.006 0.002 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (12972) covalent geometry : angle 0.84445 / 0.41 (18432) hydrogen bonds : bond 0.04715 / 2.98 ( 604) hydrogen bonds : angle 3.99628 / 2.88 ( 1598) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6493 (m-80) cc_final: 0.6231 (m-80) REVERT: G 1563 ARG cc_start: 0.7105 (mtt90) cc_final: 0.6787 (mtt90) REVERT: G 1585 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7133 (mmm) REVERT: O 38 ASN cc_start: 0.7749 (t0) cc_final: 0.7517 (t0) REVERT: R 57 VAL cc_start: 0.8075 (t) cc_final: 0.7805 (m) REVERT: R 77 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7565 (mttt) outliers start: 20 outliers final: 17 residues processed: 143 average time/residue: 0.1191 time to fit residues: 23.3292 Evaluate side-chains 139 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1585 MET Chi-restraints excluded: chain G residue 1621 ILE Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain G residue 1639 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 25 ASN Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 49 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117112 restraints weight = 17740.090| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 0.99 r_work: 0.3448 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12973 Z= 0.138 Angle : 0.796 30.955 18432 Z= 0.383 Chirality : 0.043 0.237 2078 Planarity : 0.004 0.038 1571 Dihedral : 29.153 120.437 3441 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.03 % Allowed : 16.21 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.27), residues: 946 helix: 0.99 (0.21), residues: 600 sheet: 0.34 (0.83), residues: 47 loop : -0.25 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 78 TYR 0.079 0.002 TYR P 80 PHE 0.012 0.001 PHE P 67 TRP 0.016 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (12972) covalent geometry : angle 0.79579 / 0.38 (18432) hydrogen bonds : bond 0.04017 / 2.52 ( 604) hydrogen bonds : angle 3.86124 / 2.77 ( 1598) Misc. bond : bond 0.00077 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6437 (m-80) cc_final: 0.6053 (m-80) REVERT: G 1563 ARG cc_start: 0.7143 (mtt90) cc_final: 0.6852 (mtt90) REVERT: G 1585 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.7043 (mmm) REVERT: O 38 ASN cc_start: 0.7729 (t0) cc_final: 0.7491 (t0) REVERT: O 99 ARG cc_start: 0.7845 (mmt-90) cc_final: 0.7396 (mtp85) REVERT: P 56 MET cc_start: 0.7299 (tpp) cc_final: 0.7072 (mmm) REVERT: R 57 VAL cc_start: 0.8043 (t) cc_final: 0.7787 (m) REVERT: R 77 LYS cc_start: 0.7828 (mtmt) cc_final: 0.7545 (mttt) outliers start: 17 outliers final: 15 residues processed: 136 average time/residue: 0.1268 time to fit residues: 23.6563 Evaluate side-chains 138 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1585 MET Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 25 ASN Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116376 restraints weight = 17589.719| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 0.99 r_work: 0.3438 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12973 Z= 0.154 Angle : 0.806 31.086 18432 Z= 0.388 Chirality : 0.044 0.236 2078 Planarity : 0.005 0.038 1571 Dihedral : 29.131 117.916 3441 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.62 % Allowed : 15.73 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.27), residues: 946 helix: 0.91 (0.21), residues: 601 sheet: 0.37 (0.83), residues: 47 loop : -0.34 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 78 TYR 0.078 0.003 TYR P 80 PHE 0.013 0.001 PHE Q 67 TRP 0.014 0.002 TRP G1650 HIS 0.005 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (12972) covalent geometry : angle 0.80610 / 0.39 (18432) hydrogen bonds : bond 0.04213 / 2.65 ( 604) hydrogen bonds : angle 3.89090 / 2.80 ( 1598) Misc. bond : bond 0.00057 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3406.42 seconds wall clock time: 58 minutes 51.87 seconds (3531.87 seconds total)