Starting phenix.real_space_refine on Wed Aug 5 23:14:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oos_17027/08_2026/8oos_17027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oos_17027/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8oos_17027/08_2026/8oos_17027.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oos_17027/08_2026/8oos_17027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oos_17027/08_2026/8oos_17027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oos_17027/08_2026/8oos_17027.map" model { file = "/net/cci-nas-00/data/ceres_data/8oos_17027/08_2026/8oos_17027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oos_17027/08_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-2.2rc3-6140/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: 2.44, per 1000 atoms: 0.20 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: 1.08 Conformation dependent library (CDL) restraints added in 406.6 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: 1.50 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: 2.20 Time building geometry restraints manager: 1.46 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: 0.000 Normalize map: mean=0, sd=1: 3.280 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.430 Find NCS groups from input model: 0.060 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- 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= 0.594 Angle : 1.288 70.779 18432 Z= 0.664 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 1.28835 / 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 : 0.255 Fit side-chains revert: symmetry clash REVERT: G 1258 MET cc_start: 0.4246 (mmm) cc_final: 0.3209 (ptt) REVERT: G 1262 MET cc_start: 0.5481 (tpp) cc_final: 0.5178 (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: 0.7037 (tpt90) REVERT: O 38 ASN cc_start: 0.7476 (t0) cc_final: 0.7153 (t0) REVERT: O 94 ASN cc_start: 0.7548 (t0) cc_final: 0.7273 (t0) REVERT: O 99 ARG cc_start: 0.7462 (mmt-90) cc_final: 0.6810 (mtp85) REVERT: P 40 LYS cc_start: 0.7836 (mttt) cc_final: 0.7420 (mmtp) REVERT: P 65 ASP cc_start: 0.7484 (t70) cc_final: 0.7087 (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: 0.1474 time to fit residues: 41.5684 Evaluate side-chains 152 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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: 10.0000 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 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: 5.9990 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 = 0.3742 r_free = 0.3742 target = 0.131310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114337 restraints weight = 17488.520| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 0.96 r_work: 0.3408 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12973 Z= 0.219 Angle : 0.969 30.584 18432 Z= 0.479 Chirality : 0.055 0.241 2078 Planarity : 0.006 0.050 1571 Dihedral : 29.421 137.945 3441 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.43 % Allowed : 7.39 % Favored : 91.18 % 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: -0.51 (0.26), residues: 946 helix: -0.27 (0.20), residues: 588 sheet: 0.75 (0.86), residues: 42 loop : -0.29 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G1661 TYR 0.022 0.003 TYR O 50 PHE 0.021 0.003 PHE G1079 TRP 0.018 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 0.96889 / 0.48 (18432) hydrogen bonds : bond 0.06327 / 4.04 ( 604) hydrogen bonds : angle 4.48850 / 3.24 ( 1598) Misc. bond : bond 0.01359 / 0.72 ( 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 159 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1230 TYR cc_start: 0.4750 (t80) cc_final: 0.4030 (t80) REVERT: G 1240 MET cc_start: 0.1406 (OUTLIER) cc_final: 0.0912 (ppp) REVERT: G 1264 PHE cc_start: 0.6181 (m-80) cc_final: 0.5886 (m-80) REVERT: O 38 ASN cc_start: 0.7640 (t0) cc_final: 0.7424 (t0) REVERT: R 57 VAL cc_start: 0.8106 (t) cc_final: 0.7734 (m) REVERT: R 77 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7436 (mttt) outliers start: 12 outliers final: 8 residues processed: 156 average time/residue: 0.1349 time to fit residues: 27.8141 Evaluate side-chains 146 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 111 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 = 0.133858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116684 restraints weight = 17659.127| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.00 r_work: 0.3428 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12973 Z= 0.171 Angle : 0.856 31.471 18432 Z= 0.422 Chirality : 0.048 0.255 2078 Planarity : 0.005 0.040 1571 Dihedral : 29.585 132.799 3441 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.67 % Allowed : 9.42 % Favored : 88.92 % 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: 0.08 (0.27), residues: 946 helix: 0.28 (0.20), residues: 593 sheet: 0.69 (0.87), residues: 42 loop : -0.23 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G1201 TYR 0.046 0.002 TYR N 88 PHE 0.015 0.002 PHE G1079 TRP 0.011 0.002 TRP G1650 HIS 0.006 0.001 HIS P 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (12972) covalent geometry : angle 0.85583 / 0.42 (18432) hydrogen bonds : bond 0.05323 / 3.37 ( 604) hydrogen bonds : angle 4.06647 / 2.93 ( 1598) Misc. bond : bond 0.00280 / 0.15 ( 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 146 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: G 1563 ARG cc_start: 0.7110 (mtt90) cc_final: 0.6720 (mtt90) REVERT: G 1585 MET cc_start: 0.7288 (tpp) cc_final: 0.6961 (tpp) REVERT: G 1650 TRP cc_start: 0.5751 (OUTLIER) cc_final: 0.5524 (t60) REVERT: O 38 ASN cc_start: 0.7736 (t0) cc_final: 0.7503 (t0) REVERT: P 56 MET cc_start: 0.7196 (tpp) cc_final: 0.6784 (mmm) REVERT: R 57 VAL cc_start: 0.8062 (t) cc_final: 0.7741 (m) REVERT: R 77 LYS cc_start: 0.7782 (mtmt) cc_final: 0.7460 (mttt) outliers start: 14 outliers final: 7 residues processed: 145 average time/residue: 0.1258 time to fit residues: 24.4554 Evaluate side-chains 132 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 1650 TRP Chi-restraints excluded: chain M residue 117 VAL 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: 10.0000 chunk 44 optimal weight: 9.9990 chunk 101 optimal weight: 0.0270 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117694 restraints weight = 17593.481| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.00 r_work: 0.3446 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3068 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= 0.146 Angle : 0.816 30.968 18432 Z= 0.398 Chirality : 0.046 0.254 2078 Planarity : 0.004 0.039 1571 Dihedral : 29.416 131.059 3441 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.67 % Allowed : 11.80 % Favored : 86.53 % 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: 0.57 (0.27), residues: 946 helix: 0.73 (0.21), residues: 593 sheet: 0.29 (0.83), residues: 47 loop : -0.07 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G1265 TYR 0.026 0.002 TYR N 88 PHE 0.013 0.001 PHE M 67 TRP 0.014 0.003 TRP G1021 HIS 0.012 0.001 HIS G1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (12972) covalent geometry : angle 0.81591 / 0.40 (18432) hydrogen bonds : bond 0.04429 / 2.79 ( 604) hydrogen bonds : angle 3.87518 / 2.80 ( 1598) Misc. bond : bond 0.00010 / 0.01 ( 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 148 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: G 1230 TYR cc_start: 0.4759 (t80) cc_final: 0.3876 (t80) REVERT: G 1264 PHE cc_start: 0.6634 (m-80) cc_final: 0.6312 (m-80) REVERT: G 1563 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6871 (mtt90) REVERT: G 1650 TRP cc_start: 0.5655 (OUTLIER) cc_final: 0.5451 (t60) REVERT: N 25 ASN cc_start: 0.7120 (m-40) cc_final: 0.6719 (m-40) REVERT: O 38 ASN cc_start: 0.7718 (t0) cc_final: 0.7455 (t0) REVERT: P 56 MET cc_start: 0.7190 (tpp) cc_final: 0.6919 (mmm) REVERT: P 110 GLU cc_start: 0.7941 (tp30) cc_final: 0.7733 (tp30) REVERT: R 57 VAL cc_start: 0.8035 (t) cc_final: 0.7738 (m) REVERT: R 77 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7468 (mttt) outliers start: 14 outliers final: 5 residues processed: 142 average time/residue: 0.1400 time to fit residues: 26.7122 Evaluate side-chains 128 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 84 optimal weight: 0.0570 chunk 109 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.134293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117167 restraints weight = 17603.585| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.00 r_work: 0.3445 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3269 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= 0.144 Angle : 0.804 30.853 18432 Z= 0.390 Chirality : 0.045 0.260 2078 Planarity : 0.004 0.037 1571 Dihedral : 29.315 127.674 3441 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.03 % Allowed : 13.23 % Favored : 84.74 % 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: 0.76 (0.27), residues: 946 helix: 0.91 (0.21), residues: 593 sheet: 0.25 (0.82), residues: 47 loop : -0.05 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1017 TYR 0.022 0.002 TYR N 88 PHE 0.012 0.001 PHE M 67 TRP 0.012 0.002 TRP G1650 HIS 0.007 0.001 HIS G1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (12972) covalent geometry : angle 0.80432 / 0.39 (18432) hydrogen bonds : bond 0.04279 / 2.69 ( 604) hydrogen bonds : angle 3.80035 / 2.76 ( 1598) Misc. bond : bond 0.00041 / 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 145 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: G 1230 TYR cc_start: 0.4807 (t80) cc_final: 0.4336 (t80) REVERT: G 1264 PHE cc_start: 0.6595 (m-80) cc_final: 0.6243 (m-80) REVERT: G 1563 ARG cc_start: 0.7123 (mtt90) cc_final: 0.6872 (mtt90) REVERT: O 38 ASN cc_start: 0.7704 (t0) cc_final: 0.7439 (t0) REVERT: P 56 MET cc_start: 0.7170 (tpp) cc_final: 0.6958 (mmm) REVERT: P 110 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: R 57 VAL cc_start: 0.8026 (t) cc_final: 0.7748 (m) REVERT: R 77 LYS cc_start: 0.7805 (mtmt) cc_final: 0.7483 (mttt) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 0.1306 time to fit residues: 24.1413 Evaluate side-chains 134 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 1240 MET Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 110 GLU Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain Q residue 117 VAL 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: 0.5980 chunk 103 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.134256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117158 restraints weight = 17548.254| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 0.99 r_work: 0.3442 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3441 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= 0.147 Angle : 0.809 31.070 18432 Z= 0.390 Chirality : 0.045 0.248 2078 Planarity : 0.004 0.037 1571 Dihedral : 29.255 125.018 3441 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.26 % Allowed : 13.83 % Favored : 83.91 % 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: 0.79 (0.27), residues: 946 helix: 0.94 (0.21), residues: 594 sheet: 0.35 (0.83), residues: 47 loop : -0.07 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1017 TYR 0.017 0.002 TYR N 88 PHE 0.012 0.001 PHE M 67 TRP 0.016 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (12972) covalent geometry : angle 0.80889 / 0.39 (18432) hydrogen bonds : bond 0.04202 / 2.65 ( 604) hydrogen bonds : angle 3.77338 / 2.72 ( 1598) Misc. bond : bond 0.00024 / 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 143 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6645 (m-80) cc_final: 0.5851 (m-10) REVERT: G 1563 ARG cc_start: 0.7124 (mtt90) cc_final: 0.6885 (mtt90) REVERT: O 38 ASN cc_start: 0.7753 (t0) cc_final: 0.7519 (t0) REVERT: P 56 MET cc_start: 0.7136 (tpp) cc_final: 0.6893 (mmm) REVERT: P 110 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: R 57 VAL cc_start: 0.8076 (t) cc_final: 0.7804 (m) REVERT: R 77 LYS cc_start: 0.7828 (mtmt) cc_final: 0.7541 (mttt) outliers start: 19 outliers final: 12 residues processed: 140 average time/residue: 0.1155 time to fit residues: 22.2380 Evaluate side-chains 134 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 1635 ILE 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 P residue 110 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116270 restraints weight = 17517.494| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.00 r_work: 0.3436 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12973 Z= 0.156 Angle : 0.819 31.311 18432 Z= 0.393 Chirality : 0.045 0.234 2078 Planarity : 0.004 0.039 1571 Dihedral : 29.224 123.362 3441 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.15 % Allowed : 15.49 % 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: 0.71 (0.27), residues: 946 helix: 0.90 (0.21), residues: 595 sheet: 0.28 (0.83), residues: 47 loop : -0.16 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1664 TYR 0.015 0.002 TYR O 50 PHE 0.013 0.002 PHE G1079 TRP 0.014 0.002 TRP G1650 HIS 0.006 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (12972) covalent geometry : angle 0.81948 / 0.39 (18432) hydrogen bonds : bond 0.04264 / 2.70 ( 604) hydrogen bonds : angle 3.78014 / 2.72 ( 1598) Misc. bond : bond 0.00028 / 0.01 ( 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 140 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6694 (m-80) cc_final: 0.5969 (m-10) REVERT: G 1563 ARG cc_start: 0.7199 (mtt90) cc_final: 0.6891 (mtt90) REVERT: O 38 ASN cc_start: 0.7730 (t0) cc_final: 0.7493 (t0) REVERT: P 56 MET cc_start: 0.7144 (tpp) cc_final: 0.6943 (mmm) REVERT: R 57 VAL cc_start: 0.8063 (t) cc_final: 0.7787 (m) REVERT: R 77 LYS cc_start: 0.7859 (mtmt) cc_final: 0.7563 (mttt) outliers start: 18 outliers final: 13 residues processed: 137 average time/residue: 0.1123 time to fit residues: 21.1541 Evaluate side-chains 131 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 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 1635 ILE 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 58 THR Chi-restraints excluded: chain Q residue 117 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: 0.9980 chunk 41 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.134130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116973 restraints weight = 17519.579| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 0.99 r_work: 0.3443 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12973 Z= 0.144 Angle : 0.805 31.001 18432 Z= 0.386 Chirality : 0.044 0.225 2078 Planarity : 0.004 0.038 1571 Dihedral : 29.112 122.642 3441 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.03 % Allowed : 15.61 % 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: 0.86 (0.27), residues: 946 helix: 1.03 (0.21), residues: 594 sheet: 0.40 (0.84), residues: 47 loop : -0.11 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1017 TYR 0.039 0.002 TYR N 88 PHE 0.015 0.001 PHE G1264 TRP 0.012 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (12972) covalent geometry : angle 0.80454 / 0.39 (18432) hydrogen bonds : bond 0.04094 / 2.59 ( 604) hydrogen bonds : angle 3.80024 / 2.74 ( 1598) Misc. bond : bond 0.00044 / 0.02 ( 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: 17 poor density : 124 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6876 (m-80) cc_final: 0.6606 (m-80) REVERT: G 1563 ARG cc_start: 0.7116 (mtt90) cc_final: 0.6890 (mtt90) REVERT: O 38 ASN cc_start: 0.7720 (t0) cc_final: 0.7480 (t0) REVERT: P 110 GLU cc_start: 0.7997 (tp30) cc_final: 0.7753 (tp30) REVERT: R 57 VAL cc_start: 0.8067 (t) cc_final: 0.7796 (m) REVERT: R 77 LYS cc_start: 0.7872 (mtmt) cc_final: 0.7566 (mttt) outliers start: 17 outliers final: 16 residues processed: 137 average time/residue: 0.1100 time to fit residues: 20.6554 Evaluate side-chains 134 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 1635 ILE 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 58 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.134224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117117 restraints weight = 17567.201| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.00 r_work: 0.3451 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12973 Z= 0.143 Angle : 0.800 30.950 18432 Z= 0.385 Chirality : 0.044 0.227 2078 Planarity : 0.004 0.038 1571 Dihedral : 29.025 120.432 3441 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.15 % Allowed : 16.33 % Favored : 81.53 % 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: 0.83 (0.27), residues: 946 helix: 1.00 (0.21), residues: 596 sheet: 0.40 (0.84), residues: 47 loop : -0.14 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 92 TYR 0.061 0.002 TYR N 88 PHE 0.012 0.001 PHE G1264 TRP 0.011 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (12972) covalent geometry : angle 0.79976 / 0.38 (18432) hydrogen bonds : bond 0.04095 / 2.59 ( 604) hydrogen bonds : angle 3.82258 / 2.74 ( 1598) Misc. bond : bond 0.00046 / 0.02 ( 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 139 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6899 (m-80) cc_final: 0.6679 (m-80) REVERT: O 38 ASN cc_start: 0.7688 (t0) cc_final: 0.7366 (t0) REVERT: P 110 GLU cc_start: 0.7978 (tp30) cc_final: 0.7737 (tp30) REVERT: R 57 VAL cc_start: 0.8049 (t) cc_final: 0.7787 (m) REVERT: R 77 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7573 (mttt) outliers start: 18 outliers final: 16 residues processed: 134 average time/residue: 0.1201 time to fit residues: 22.0101 Evaluate side-chains 134 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 1635 ILE 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 58 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 105 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1191 HIS O 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117600 restraints weight = 17693.171| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.00 r_work: 0.3449 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12973 Z= 0.141 Angle : 0.800 30.933 18432 Z= 0.384 Chirality : 0.043 0.231 2078 Planarity : 0.004 0.037 1571 Dihedral : 28.973 118.661 3441 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.03 % Allowed : 16.57 % Favored : 81.41 % 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: 0.88 (0.27), residues: 946 helix: 1.05 (0.21), residues: 596 sheet: 0.45 (0.84), residues: 47 loop : -0.16 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1664 TYR 0.041 0.002 TYR N 88 PHE 0.013 0.001 PHE P 67 TRP 0.012 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (12972) covalent geometry : angle 0.80031 / 0.38 (18432) hydrogen bonds : bond 0.04038 / 2.55 ( 604) hydrogen bonds : angle 3.82368 / 2.75 ( 1598) Misc. bond : bond 0.00056 / 0.03 ( 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 137 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6939 (m-80) cc_final: 0.6735 (m-80) REVERT: G 1650 TRP cc_start: 0.5626 (OUTLIER) cc_final: 0.5260 (t60) REVERT: O 38 ASN cc_start: 0.7696 (t0) cc_final: 0.7351 (t0) REVERT: O 99 ARG cc_start: 0.7825 (mmt-90) cc_final: 0.7402 (mtp180) REVERT: P 110 GLU cc_start: 0.7987 (tp30) cc_final: 0.7750 (tp30) REVERT: R 57 VAL cc_start: 0.8055 (t) cc_final: 0.7790 (m) REVERT: R 77 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7574 (mttt) outliers start: 17 outliers final: 13 residues processed: 131 average time/residue: 0.1077 time to fit residues: 19.3383 Evaluate side-chains 131 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 1635 ILE 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 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 70 VAL 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: 0.6980 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116685 restraints weight = 17516.308| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.00 r_work: 0.3443 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12973 Z= 0.152 Angle : 0.807 31.099 18432 Z= 0.387 Chirality : 0.044 0.240 2078 Planarity : 0.004 0.038 1571 Dihedral : 28.994 116.861 3441 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.15 % Allowed : 16.33 % Favored : 81.53 % 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: 0.74 (0.27), residues: 946 helix: 0.95 (0.21), residues: 596 sheet: 0.43 (0.84), residues: 47 loop : -0.22 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1664 TYR 0.046 0.002 TYR N 88 PHE 0.013 0.002 PHE G1264 TRP 0.012 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (12972) covalent geometry : angle 0.80669 / 0.39 (18432) hydrogen bonds : bond 0.04190 / 2.65 ( 604) hydrogen bonds : angle 3.88309 / 2.79 ( 1598) Misc. bond : bond 0.00042 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2852.31 seconds wall clock time: 49 minutes 17.88 seconds (2957.88 seconds total)