Starting phenix.real_space_refine on Sat Aug 23 13:09:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oos_17027/08_2025/8oos_17027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oos_17027/08_2025/8oos_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_17027/08_2025/8oos_17027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oos_17027/08_2025/8oos_17027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oos_17027/08_2025/8oos_17027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oos_17027/08_2025/8oos_17027.map" } 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-2.0-5787/lib/python3.9/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: 2.64, 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: 0.68 Conformation dependent library (CDL) restraints added in 417.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.75 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: 2.60 Time building geometry restraints manager: 0.98 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=" C2' DG K 25 " pdb=" C1' DG K 25 " ideal model delta sigma weight residual 1.525 1.479 0.046 2.00e-02 2.50e+03 5.39e+00 ... (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: 1404 0.050 - 0.100: 553 0.100 - 0.150: 104 0.150 - 0.200: 16 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 2.42 2.24 0.18 2.00e-01 2.50e+01 7.76e-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: 4.500 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.020 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.330 12973 Z= 0.432 Angle : 1.289 70.779 18432 Z= 0.612 Chirality : 0.051 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 aren 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 covalent geometry : bond 0.00696 (12972) covalent geometry : angle 1.28882 (18432) hydrogen bonds : bond 0.22571 ( 604) hydrogen bonds : angle 8.28872 ( 1598) Misc. bond : bond 0.32952 ( 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 : 0.308 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: 0.7485 (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: 0.1586 time to fit residues: 44.1652 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 : 0.361 ------------------------------------------------------------------------------- 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: 3.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1087 GLN G1186 GLN G1577 GLN M 68 GLN P 60 ASN P 81 ASN Q 113 HIS R 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116078 restraints weight = 17495.790| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 0.99 r_work: 0.3419 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12973 Z= 0.222 Angle : 0.854 31.814 18432 Z= 0.427 Chirality : 0.042 0.191 2078 Planarity : 0.005 0.043 1571 Dihedral : 29.358 128.871 3441 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.19 % Allowed : 7.63 % 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 aren not related in a simple way. whole: -0.23 (0.26), residues: 946 helix: -0.10 (0.20), residues: 588 sheet: 0.81 (0.86), residues: 42 loop : -0.04 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G1664 TYR 0.024 0.002 TYR O 50 PHE 0.017 0.002 PHE G1079 TRP 0.027 0.002 TRP G1650 HIS 0.006 0.001 HIS G1663 Details of bonding type rmsd covalent geometry : bond 0.00498 (12972) covalent geometry : angle 0.85360 (18432) hydrogen bonds : bond 0.05050 ( 604) hydrogen bonds : angle 4.16459 ( 1598) Misc. bond : bond 0.00491 ( 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 156 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1186 GLN cc_start: 0.3947 (OUTLIER) cc_final: 0.3647 (mp10) REVERT: G 1258 MET cc_start: 0.3848 (mmm) cc_final: 0.3565 (mtt) REVERT: N 25 ASN cc_start: 0.7100 (m-40) cc_final: 0.6653 (m110) REVERT: O 38 ASN cc_start: 0.7720 (t0) cc_final: 0.7499 (t0) REVERT: R 57 VAL cc_start: 0.8024 (t) cc_final: 0.7757 (m) REVERT: R 77 LYS cc_start: 0.7713 (mtmt) cc_final: 0.7433 (mttt) outliers start: 10 outliers final: 8 residues processed: 154 average time/residue: 0.1318 time to fit residues: 26.7219 Evaluate side-chains 140 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 1635 ILE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 121 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: 3.9990 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113750 restraints weight = 17799.239| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 0.99 r_work: 0.3391 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12973 Z= 0.233 Angle : 0.851 31.633 18432 Z= 0.421 Chirality : 0.042 0.223 2078 Planarity : 0.006 0.042 1571 Dihedral : 29.232 128.060 3441 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.38 % Allowed : 10.25 % Favored : 87.37 % 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 aren not related in a simple way. whole: 0.02 (0.27), residues: 946 helix: 0.25 (0.20), residues: 588 sheet: 0.04 (0.82), residues: 47 loop : -0.16 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G1664 TYR 0.032 0.002 TYR N 88 PHE 0.022 0.002 PHE G1079 TRP 0.018 0.003 TRP G1650 HIS 0.006 0.002 HIS G1663 Details of bonding type rmsd covalent geometry : bond 0.00531 (12972) covalent geometry : angle 0.85082 (18432) hydrogen bonds : bond 0.04995 ( 604) hydrogen bonds : angle 4.12557 ( 1598) Misc. bond : bond 0.00185 ( 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 152 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: G 1264 PHE cc_start: 0.6425 (m-80) cc_final: 0.6159 (m-80) REVERT: G 1545 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5770 (mmm) REVERT: G 1563 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6829 (mtt90) REVERT: R 57 VAL cc_start: 0.8111 (t) cc_final: 0.7848 (m) REVERT: R 77 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7461 (mttt) outliers start: 20 outliers final: 11 residues processed: 147 average time/residue: 0.1254 time to fit residues: 24.8393 Evaluate side-chains 136 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 1650 TRP Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 101 optimal weight: 0.0370 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 16 optimal weight: 0.0000 chunk 80 optimal weight: 0.9980 overall best weight: 0.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1186 GLN G1269 ASN M 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118379 restraints weight = 17667.050| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.00 r_work: 0.3461 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12973 Z= 0.143 Angle : 0.748 30.081 18432 Z= 0.362 Chirality : 0.035 0.170 2078 Planarity : 0.004 0.036 1571 Dihedral : 28.491 120.947 3441 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.79 % Allowed : 11.32 % Favored : 86.89 % 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 aren not related in a simple way. whole: 0.84 (0.27), residues: 946 helix: 1.01 (0.21), residues: 593 sheet: 0.17 (0.82), residues: 47 loop : -0.09 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1234 TYR 0.028 0.001 TYR N 88 PHE 0.014 0.001 PHE P 67 TRP 0.013 0.002 TRP G1650 HIS 0.005 0.001 HIS P 79 Details of bonding type rmsd covalent geometry : bond 0.00308 (12972) covalent geometry : angle 0.74768 (18432) hydrogen bonds : bond 0.03613 ( 604) hydrogen bonds : angle 3.60241 ( 1598) Misc. bond : bond 0.00068 ( 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 151 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7157 (m100) cc_final: 0.6904 (m100) REVERT: G 1545 MET cc_start: 0.6427 (ttp) cc_final: 0.5908 (mmm) REVERT: G 1563 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.6911 (mtm-85) REVERT: G 1650 TRP cc_start: 0.5752 (OUTLIER) cc_final: 0.5512 (t60) REVERT: N 25 ASN cc_start: 0.7229 (m-40) cc_final: 0.6852 (m110) REVERT: N 57 VAL cc_start: 0.8119 (t) cc_final: 0.7868 (m) REVERT: R 57 VAL cc_start: 0.8085 (t) cc_final: 0.7841 (m) REVERT: R 68 ASP cc_start: 0.8070 (m-30) cc_final: 0.7857 (m-30) REVERT: R 77 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7443 (mttt) outliers start: 15 outliers final: 8 residues processed: 147 average time/residue: 0.1179 time to fit residues: 23.1997 Evaluate side-chains 133 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL 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 G residue 1669 LYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 56 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1191 HIS G1207 GLN P 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114411 restraints weight = 17760.767| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 0.99 r_work: 0.3402 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12973 Z= 0.212 Angle : 0.815 31.864 18432 Z= 0.399 Chirality : 0.039 0.218 2078 Planarity : 0.005 0.038 1571 Dihedral : 28.917 117.697 3441 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.74 % Allowed : 12.04 % Favored : 85.22 % 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 aren not related in a simple way. whole: 0.65 (0.27), residues: 946 helix: 0.88 (0.21), residues: 587 sheet: -0.01 (0.81), residues: 47 loop : -0.19 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 72 TYR 0.038 0.002 TYR N 88 PHE 0.023 0.002 PHE G1264 TRP 0.015 0.002 TRP G1650 HIS 0.006 0.001 HIS G1663 Details of bonding type rmsd covalent geometry : bond 0.00479 (12972) covalent geometry : angle 0.81498 (18432) hydrogen bonds : bond 0.04485 ( 604) hydrogen bonds : angle 3.90126 ( 1598) Misc. bond : bond 0.00031 ( 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 146 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7193 (m100) cc_final: 0.6965 (m100) REVERT: G 1258 MET cc_start: 0.3921 (mmm) cc_final: 0.3651 (mtt) REVERT: R 57 VAL cc_start: 0.8091 (t) cc_final: 0.7839 (m) REVERT: R 77 LYS cc_start: 0.7769 (mtmt) cc_final: 0.7490 (mttt) outliers start: 23 outliers final: 18 residues processed: 141 average time/residue: 0.1074 time to fit residues: 21.1767 Evaluate side-chains 133 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain G residue 1650 TRP Chi-restraints excluded: chain G residue 1653 THR Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 121 SER 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 50 ILE Chi-restraints excluded: chain R residue 70 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: 0.1980 chunk 103 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 81 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1141 ASN G1191 HIS P 60 ASN P 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117909 restraints weight = 17627.700| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 0.97 r_work: 0.3450 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: 0.7132 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12973 Z= 0.145 Angle : 0.752 30.465 18432 Z= 0.363 Chirality : 0.035 0.172 2078 Planarity : 0.005 0.087 1571 Dihedral : 28.453 114.964 3441 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.15 % Allowed : 13.47 % Favored : 84.39 % 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 aren not related in a simple way. whole: 1.12 (0.28), residues: 946 helix: 1.26 (0.21), residues: 588 sheet: 0.13 (0.81), residues: 47 loop : -0.00 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1661 TYR 0.054 0.002 TYR N 88 PHE 0.023 0.001 PHE G1264 TRP 0.014 0.001 TRP G1650 HIS 0.007 0.001 HIS P 79 Details of bonding type rmsd covalent geometry : bond 0.00311 (12972) covalent geometry : angle 0.75162 (18432) hydrogen bonds : bond 0.03680 ( 604) hydrogen bonds : angle 3.67392 ( 1598) Misc. bond : bond 0.00083 ( 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: 18 poor density : 121 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7171 (m100) cc_final: 0.6886 (m100) REVERT: G 1216 ILE cc_start: 0.8119 (mp) cc_final: 0.7917 (mp) REVERT: G 1545 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6157 (mmm) REVERT: G 1563 ARG cc_start: 0.7103 (mtm-85) cc_final: 0.6847 (mtt90) REVERT: M 73 GLU cc_start: 0.7478 (tt0) cc_final: 0.7237 (tt0) REVERT: P 79 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6741 (t-90) REVERT: R 57 VAL cc_start: 0.8080 (t) cc_final: 0.7845 (m) REVERT: R 77 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7470 (mttt) outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 0.1222 time to fit residues: 22.0878 Evaluate side-chains 128 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain G residue 1661 ARG Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 79 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1151 HIS G1191 HIS P 60 ASN P 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113716 restraints weight = 17700.257| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 0.97 r_work: 0.3396 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4051 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= 0.228 Angle : 0.826 32.002 18432 Z= 0.407 Chirality : 0.040 0.209 2078 Planarity : 0.006 0.090 1571 Dihedral : 29.013 114.074 3441 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.10 % Allowed : 13.95 % Favored : 82.96 % 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 aren not related in a simple way. whole: 0.48 (0.27), residues: 946 helix: 0.80 (0.21), residues: 589 sheet: -0.09 (0.80), residues: 47 loop : -0.37 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G1661 TYR 0.046 0.003 TYR N 88 PHE 0.031 0.002 PHE G1264 TRP 0.020 0.002 TRP G1650 HIS 0.009 0.002 HIS G1151 Details of bonding type rmsd covalent geometry : bond 0.00520 (12972) covalent geometry : angle 0.82572 (18432) hydrogen bonds : bond 0.04704 ( 604) hydrogen bonds : angle 3.98335 ( 1598) Misc. bond : bond 0.00014 ( 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 141 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: G 1018 TYR cc_start: 0.7081 (m-10) cc_final: 0.6696 (m-10) REVERT: G 1021 TRP cc_start: 0.7213 (m100) cc_final: 0.6926 (m100) REVERT: G 1216 ILE cc_start: 0.8052 (mp) cc_final: 0.7814 (mp) REVERT: G 1258 MET cc_start: 0.3747 (mmm) cc_final: 0.3521 (mtt) REVERT: G 1545 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6089 (mmm) REVERT: G 1650 TRP cc_start: 0.5820 (OUTLIER) cc_final: 0.5590 (t60) REVERT: R 57 VAL cc_start: 0.8085 (t) cc_final: 0.7828 (m) REVERT: R 77 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7509 (mttt) outliers start: 26 outliers final: 22 residues processed: 136 average time/residue: 0.1175 time to fit residues: 21.9993 Evaluate side-chains 138 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain G residue 1650 TRP Chi-restraints excluded: chain G residue 1653 THR Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 56 LYS 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 50 ILE Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 80 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 0.0060 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1080 HIS G1191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116151 restraints weight = 17637.199| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 0.97 r_work: 0.3435 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12973 Z= 0.160 Angle : 0.762 31.075 18432 Z= 0.370 Chirality : 0.036 0.184 2078 Planarity : 0.004 0.064 1571 Dihedral : 28.634 111.298 3441 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.03 % Allowed : 15.02 % Favored : 82.96 % 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 aren not related in a simple way. whole: 0.81 (0.27), residues: 946 helix: 1.06 (0.21), residues: 595 sheet: 0.02 (0.80), residues: 47 loop : -0.26 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1661 TYR 0.049 0.002 TYR N 88 PHE 0.030 0.002 PHE G1264 TRP 0.019 0.002 TRP G1650 HIS 0.005 0.001 HIS G1663 Details of bonding type rmsd covalent geometry : bond 0.00352 (12972) covalent geometry : angle 0.76241 (18432) hydrogen bonds : bond 0.03920 ( 604) hydrogen bonds : angle 3.76920 ( 1598) Misc. bond : bond 0.00055 ( 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 134 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7152 (m100) cc_final: 0.6878 (m100) REVERT: G 1258 MET cc_start: 0.3761 (mmm) cc_final: 0.3390 (mtt) REVERT: G 1545 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6254 (mmm) REVERT: G 1563 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.6752 (mtt90) REVERT: M 73 GLU cc_start: 0.7515 (tt0) cc_final: 0.7285 (tt0) REVERT: R 57 VAL cc_start: 0.8088 (t) cc_final: 0.7840 (m) REVERT: R 77 LYS cc_start: 0.7805 (mtmt) cc_final: 0.7497 (mttt) outliers start: 17 outliers final: 15 residues processed: 131 average time/residue: 0.1102 time to fit residues: 19.6226 Evaluate side-chains 129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain G residue 1653 THR Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 80 TYR 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 73 THR Chi-restraints excluded: chain R residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 0.0060 chunk 18 optimal weight: 3.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1191 HIS P 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115921 restraints weight = 17592.918| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 0.92 r_work: 0.3433 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12973 Z= 0.165 Angle : 0.762 30.980 18432 Z= 0.369 Chirality : 0.036 0.183 2078 Planarity : 0.004 0.055 1571 Dihedral : 28.604 111.490 3441 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.26 % Allowed : 15.14 % Favored : 82.60 % 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 aren not related in a simple way. whole: 0.83 (0.27), residues: 946 helix: 1.11 (0.21), residues: 596 sheet: 0.13 (0.81), residues: 47 loop : -0.37 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G1661 TYR 0.046 0.002 TYR N 88 PHE 0.031 0.002 PHE G1264 TRP 0.017 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 Details of bonding type rmsd covalent geometry : bond 0.00365 (12972) covalent geometry : angle 0.76243 (18432) hydrogen bonds : bond 0.03957 ( 604) hydrogen bonds : angle 3.74759 ( 1598) Misc. bond : bond 0.00039 ( 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 140 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7083 (m100) cc_final: 0.6877 (m100) REVERT: G 1258 MET cc_start: 0.3713 (mmm) cc_final: 0.3322 (mtt) REVERT: G 1545 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6272 (mmm) REVERT: G 1563 ARG cc_start: 0.7023 (mtm-85) cc_final: 0.6677 (mtt90) REVERT: R 57 VAL cc_start: 0.8095 (t) cc_final: 0.7855 (m) REVERT: R 77 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7492 (mttm) outliers start: 19 outliers final: 16 residues processed: 134 average time/residue: 0.1039 time to fit residues: 19.3729 Evaluate side-chains 135 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1653 THR Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain P residue 95 VAL 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 73 THR Chi-restraints excluded: chain R residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115374 restraints weight = 17820.661| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.98 r_work: 0.3422 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12973 Z= 0.181 Angle : 0.776 31.416 18432 Z= 0.377 Chirality : 0.037 0.192 2078 Planarity : 0.004 0.038 1571 Dihedral : 28.697 113.976 3441 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.03 % Allowed : 16.09 % Favored : 81.88 % 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 aren not related in a simple way. whole: 0.75 (0.27), residues: 946 helix: 1.09 (0.21), residues: 595 sheet: 0.08 (0.80), residues: 47 loop : -0.48 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 92 TYR 0.043 0.002 TYR N 88 PHE 0.032 0.002 PHE G1264 TRP 0.026 0.002 TRP G1650 HIS 0.005 0.001 HIS G1663 Details of bonding type rmsd covalent geometry : bond 0.00406 (12972) covalent geometry : angle 0.77641 (18432) hydrogen bonds : bond 0.04108 ( 604) hydrogen bonds : angle 3.81742 ( 1598) Misc. bond : bond 0.00025 ( 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 136 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7127 (m100) cc_final: 0.6890 (m100) REVERT: G 1258 MET cc_start: 0.3689 (mmm) cc_final: 0.3417 (mtt) REVERT: G 1563 ARG cc_start: 0.7043 (mtm-85) cc_final: 0.6663 (mtt90) REVERT: G 1585 MET cc_start: 0.7392 (mmm) cc_final: 0.6968 (tpp) REVERT: R 57 VAL cc_start: 0.8086 (t) cc_final: 0.7838 (m) REVERT: R 77 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7510 (mttt) outliers start: 17 outliers final: 16 residues processed: 133 average time/residue: 0.1104 time to fit residues: 20.3422 Evaluate side-chains 130 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1653 THR Chi-restraints excluded: chain G residue 1669 LYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 80 TYR 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 73 THR Chi-restraints excluded: chain R residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1191 HIS P 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114673 restraints weight = 17641.037| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 0.97 r_work: 0.3408 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12973 Z= 0.199 Angle : 0.796 31.734 18432 Z= 0.389 Chirality : 0.038 0.208 2078 Planarity : 0.005 0.038 1571 Dihedral : 28.826 117.230 3441 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.79 % Allowed : 16.45 % Favored : 81.76 % 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 aren not related in a simple way. whole: 0.53 (0.27), residues: 946 helix: 0.96 (0.21), residues: 595 sheet: 0.01 (0.81), residues: 47 loop : -0.67 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G1661 TYR 0.046 0.002 TYR N 88 PHE 0.034 0.002 PHE G1264 TRP 0.031 0.002 TRP G1650 HIS 0.005 0.001 HIS G1663 Details of bonding type rmsd covalent geometry : bond 0.00450 (12972) covalent geometry : angle 0.79615 (18432) hydrogen bonds : bond 0.04429 ( 604) hydrogen bonds : angle 3.94721 ( 1598) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2842.41 seconds wall clock time: 49 minutes 8.03 seconds (2948.03 seconds total)