Starting phenix.real_space_refine on Thu Sep 26 05:46:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/09_2024/8oos_17027.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/09_2024/8oos_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/09_2024/8oos_17027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/09_2024/8oos_17027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/09_2024/8oos_17027.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/09_2024/8oos_17027.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 7.83, per 1000 atoms: 0.64 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: 2.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 6.31 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: 5.78 Time building geometry restraints manager: 3.42 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: 2.000 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 36.010 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.840 ------------------------------------------------------------------------------- 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 : 0.007 0.117 12972 Z= 0.366 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (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 TRP 0.017 0.002 TRP G1650 HIS 0.005 0.001 HIS N 75 PHE 0.018 0.002 PHE G1096 TYR 0.052 0.007 TYR G1086 ARG 0.027 0.004 ARG G1592 *********************** 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 fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.108 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: 0.3860 time to fit residues: 107.0199 Evaluate side-chains 153 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 0.0050 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 103 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: G1087 GLN G1186 GLN M 85 GLN P 60 ASN P 81 ASN Q 113 HIS R 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12972 Z= 0.214 Angle : 0.807 30.739 18432 Z= 0.401 Chirality : 0.039 0.142 2078 Planarity : 0.005 0.035 1571 Dihedral : 29.045 135.115 3441 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.95 % Allowed : 6.44 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 946 helix: 0.25 (0.20), residues: 587 sheet: 0.99 (0.87), residues: 42 loop : 0.03 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 PHE 0.013 0.002 PHE G1096 TYR 0.016 0.002 TYR N 88 ARG 0.006 0.001 ARG G1201 *********************** 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 162 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: G 998 GLU cc_start: 0.6172 (tt0) cc_final: 0.5867 (tt0) REVERT: G 1021 TRP cc_start: 0.7062 (m100) cc_final: 0.6750 (m100) REVERT: G 1186 GLN cc_start: 0.3784 (OUTLIER) cc_final: 0.2595 (tt0) REVERT: G 1240 MET cc_start: 0.1086 (OUTLIER) cc_final: 0.0679 (ppp) REVERT: G 1585 MET cc_start: 0.6991 (tpt) cc_final: 0.6738 (tpp) REVERT: M 71 VAL cc_start: 0.6899 (t) cc_final: 0.6695 (m) REVERT: N 25 ASN cc_start: 0.6851 (m-40) cc_final: 0.6266 (m110) REVERT: O 38 ASN cc_start: 0.7719 (t0) cc_final: 0.7469 (t0) REVERT: R 57 VAL cc_start: 0.7691 (t) cc_final: 0.7301 (m) REVERT: R 77 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7345 (mttt) REVERT: R 95 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7438 (mtp85) outliers start: 8 outliers final: 5 residues processed: 158 average time/residue: 0.3499 time to fit residues: 72.0348 Evaluate side-chains 141 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 1210 LEU Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain Q residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12972 Z= 0.204 Angle : 0.779 30.727 18432 Z= 0.379 Chirality : 0.037 0.154 2078 Planarity : 0.004 0.039 1571 Dihedral : 28.795 126.622 3441 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.19 % Allowed : 9.77 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 946 helix: 0.83 (0.21), residues: 592 sheet: 0.34 (0.83), residues: 47 loop : 0.01 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G1650 HIS 0.005 0.001 HIS P 79 PHE 0.015 0.002 PHE P 67 TYR 0.018 0.002 TYR N 88 ARG 0.007 0.001 ARG O 20 *********************** 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 153 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7063 (m100) cc_final: 0.6798 (m100) REVERT: G 1230 TYR cc_start: 0.5113 (t80) cc_final: 0.4589 (t80) REVERT: G 1264 PHE cc_start: 0.6088 (m-80) cc_final: 0.5716 (m-80) REVERT: G 1563 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6725 (mtt90) REVERT: G 1585 MET cc_start: 0.7023 (tpt) cc_final: 0.6748 (tpp) REVERT: G 1650 TRP cc_start: 0.5536 (OUTLIER) cc_final: 0.5170 (t60) REVERT: N 25 ASN cc_start: 0.6951 (m-40) cc_final: 0.6435 (m110) REVERT: O 38 ASN cc_start: 0.7835 (t0) cc_final: 0.7602 (t0) REVERT: P 117 LYS cc_start: 0.7891 (tttm) cc_final: 0.7590 (ttmm) REVERT: R 57 VAL cc_start: 0.7663 (t) cc_final: 0.7347 (m) REVERT: R 77 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7386 (mttt) REVERT: R 95 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7404 (mtp85) outliers start: 10 outliers final: 6 residues processed: 149 average time/residue: 0.3301 time to fit residues: 64.8800 Evaluate side-chains 128 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 1650 TRP Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain Q residue 80 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 0.0770 chunk 110 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1186 GLN G1269 ASN P 44 GLN P 60 ASN P 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12972 Z= 0.203 Angle : 0.767 30.930 18432 Z= 0.372 Chirality : 0.037 0.174 2078 Planarity : 0.004 0.036 1571 Dihedral : 28.629 121.117 3441 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.91 % Allowed : 10.13 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 946 helix: 1.02 (0.21), residues: 593 sheet: 0.22 (0.82), residues: 47 loop : 0.00 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G1650 HIS 0.006 0.001 HIS P 79 PHE 0.016 0.002 PHE P 67 TYR 0.044 0.002 TYR N 88 ARG 0.007 0.001 ARG G1017 *********************** 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 150 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.094 Fit side-chains REVERT: G 1021 TRP cc_start: 0.7089 (m100) cc_final: 0.6774 (m100) REVERT: G 1230 TYR cc_start: 0.5030 (t80) cc_final: 0.4796 (t80) REVERT: G 1264 PHE cc_start: 0.5921 (m-80) cc_final: 0.5409 (m-80) REVERT: G 1272 ASP cc_start: 0.6466 (m-30) cc_final: 0.6181 (m-30) REVERT: G 1563 ARG cc_start: 0.6910 (mtm-85) cc_final: 0.6706 (mtm-85) REVERT: G 1585 MET cc_start: 0.7007 (tpt) cc_final: 0.6697 (tpp) REVERT: G 1650 TRP cc_start: 0.5603 (OUTLIER) cc_final: 0.5260 (t60) REVERT: N 25 ASN cc_start: 0.6847 (m-40) cc_final: 0.6261 (m-40) REVERT: N 31 LYS cc_start: 0.8136 (mttp) cc_final: 0.7917 (mttm) REVERT: O 38 ASN cc_start: 0.7900 (t0) cc_final: 0.7665 (t0) REVERT: P 80 TYR cc_start: 0.6714 (m-80) cc_final: 0.6462 (m-80) REVERT: P 117 LYS cc_start: 0.7887 (tttm) cc_final: 0.7574 (ttmm) REVERT: R 57 VAL cc_start: 0.7692 (t) cc_final: 0.7395 (m) REVERT: R 77 LYS cc_start: 0.7805 (mtmt) cc_final: 0.7422 (mttt) outliers start: 16 outliers final: 10 residues processed: 143 average time/residue: 0.3159 time to fit residues: 60.5343 Evaluate side-chains 136 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 1650 TRP Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain 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 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1141 ASN G1191 HIS N 25 ASN P 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12972 Z= 0.219 Angle : 0.775 31.552 18432 Z= 0.375 Chirality : 0.037 0.181 2078 Planarity : 0.004 0.037 1571 Dihedral : 28.633 113.328 3441 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.91 % Allowed : 12.63 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.27), residues: 946 helix: 1.04 (0.21), residues: 595 sheet: 0.13 (0.82), residues: 47 loop : -0.09 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G1650 HIS 0.003 0.001 HIS G1151 PHE 0.014 0.001 PHE Q 67 TYR 0.048 0.002 TYR N 88 ARG 0.006 0.000 ARG O 42 *********************** 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 fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7092 (m100) cc_final: 0.6880 (m100) REVERT: G 1264 PHE cc_start: 0.5928 (m-80) cc_final: 0.5581 (m-80) REVERT: G 1272 ASP cc_start: 0.6486 (m-30) cc_final: 0.6190 (m-30) REVERT: G 1563 ARG cc_start: 0.6852 (mtm-85) cc_final: 0.6636 (mtm-85) REVERT: G 1585 MET cc_start: 0.7096 (tpt) cc_final: 0.6735 (tpp) REVERT: G 1650 TRP cc_start: 0.5659 (OUTLIER) cc_final: 0.5427 (t60) REVERT: G 1684 GLU cc_start: 0.5528 (pt0) cc_final: 0.5278 (pt0) REVERT: N 31 LYS cc_start: 0.8142 (mttp) cc_final: 0.7918 (mttm) REVERT: N 77 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8174 (mtmm) REVERT: O 38 ASN cc_start: 0.7864 (t0) cc_final: 0.7618 (t0) REVERT: P 117 LYS cc_start: 0.7880 (tttm) cc_final: 0.7595 (ttmm) REVERT: R 57 VAL cc_start: 0.7733 (t) cc_final: 0.7407 (m) REVERT: R 77 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7437 (mttt) outliers start: 16 outliers final: 9 residues processed: 142 average time/residue: 0.2973 time to fit residues: 57.1107 Evaluate side-chains 135 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 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 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1191 HIS G1207 GLN G1667 GLN M 68 GLN P 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12972 Z= 0.284 Angle : 0.819 32.129 18432 Z= 0.401 Chirality : 0.039 0.214 2078 Planarity : 0.005 0.038 1571 Dihedral : 28.935 112.330 3441 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.50 % Allowed : 12.75 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 946 helix: 0.75 (0.21), residues: 594 sheet: 0.00 (0.81), residues: 47 loop : -0.33 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G1650 HIS 0.008 0.001 HIS G1151 PHE 0.020 0.002 PHE G1079 TYR 0.049 0.002 TYR N 88 ARG 0.005 0.001 ARG O 42 *********************** 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 154 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 986 LEU cc_start: 0.7339 (mp) cc_final: 0.7120 (mp) REVERT: G 1264 PHE cc_start: 0.6102 (m-80) cc_final: 0.5766 (m-80) REVERT: G 1272 ASP cc_start: 0.6481 (m-30) cc_final: 0.6198 (m-30) REVERT: G 1650 TRP cc_start: 0.5798 (OUTLIER) cc_final: 0.5560 (t60) REVERT: G 1684 GLU cc_start: 0.5515 (pt0) cc_final: 0.5241 (pt0) REVERT: N 25 ASN cc_start: 0.6799 (m110) cc_final: 0.6432 (m-40) REVERT: N 31 LYS cc_start: 0.8137 (mttp) cc_final: 0.7895 (mttm) REVERT: N 77 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8169 (mtmm) REVERT: N 92 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7460 (mtp85) REVERT: O 38 ASN cc_start: 0.7890 (t0) cc_final: 0.7669 (t0) REVERT: P 117 LYS cc_start: 0.7904 (tttm) cc_final: 0.7633 (ttmm) REVERT: R 57 VAL cc_start: 0.7713 (t) cc_final: 0.7384 (m) REVERT: R 77 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7427 (mttm) outliers start: 21 outliers final: 15 residues processed: 149 average time/residue: 0.3197 time to fit residues: 63.8190 Evaluate side-chains 143 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 1650 TRP Chi-restraints excluded: chain G residue 1653 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain 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 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1151 HIS G1191 HIS G1207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12972 Z= 0.216 Angle : 0.774 31.051 18432 Z= 0.374 Chirality : 0.037 0.188 2078 Planarity : 0.004 0.039 1571 Dihedral : 28.616 112.583 3441 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.15 % Allowed : 13.83 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 946 helix: 0.91 (0.21), residues: 595 sheet: 0.08 (0.81), residues: 47 loop : -0.32 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G1650 HIS 0.007 0.001 HIS G1151 PHE 0.015 0.002 PHE Q 67 TYR 0.045 0.002 TYR N 88 ARG 0.004 0.000 ARG O 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1216 ILE cc_start: 0.7809 (mp) cc_final: 0.7583 (mp) REVERT: G 1264 PHE cc_start: 0.6271 (m-80) cc_final: 0.5455 (m-10) REVERT: G 1272 ASP cc_start: 0.6438 (m-30) cc_final: 0.6191 (m-30) REVERT: G 1557 LYS cc_start: 0.6450 (tptp) cc_final: 0.6039 (mmtm) REVERT: G 1563 ARG cc_start: 0.6756 (mtm-85) cc_final: 0.6383 (mtt90) REVERT: G 1650 TRP cc_start: 0.5801 (OUTLIER) cc_final: 0.5539 (t60) REVERT: G 1684 GLU cc_start: 0.5595 (pt0) cc_final: 0.5292 (pt0) REVERT: N 25 ASN cc_start: 0.6731 (m110) cc_final: 0.6350 (m-40) REVERT: N 31 LYS cc_start: 0.8131 (mttp) cc_final: 0.7891 (mttm) REVERT: N 77 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8166 (mtmm) REVERT: O 38 ASN cc_start: 0.7842 (t0) cc_final: 0.7574 (t0) REVERT: O 41 GLU cc_start: 0.6403 (pm20) cc_final: 0.6104 (pm20) REVERT: O 99 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.6990 (mtp85) REVERT: P 117 LYS cc_start: 0.7954 (tttm) cc_final: 0.7623 (tttm) REVERT: R 57 VAL cc_start: 0.7720 (t) cc_final: 0.7396 (m) REVERT: R 77 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7397 (mttm) outliers start: 18 outliers final: 14 residues processed: 141 average time/residue: 0.3108 time to fit residues: 59.6784 Evaluate side-chains 140 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 1650 TRP Chi-restraints excluded: chain G residue 1653 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 25 ASN Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1191 HIS ** G1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12972 Z= 0.213 Angle : 0.773 31.466 18432 Z= 0.373 Chirality : 0.036 0.189 2078 Planarity : 0.004 0.039 1571 Dihedral : 28.576 111.238 3441 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.26 % Allowed : 14.18 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 946 helix: 0.99 (0.21), residues: 595 sheet: 0.17 (0.82), residues: 47 loop : -0.36 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G1650 HIS 0.011 0.001 HIS G1080 PHE 0.015 0.002 PHE Q 67 TYR 0.047 0.002 TYR N 88 ARG 0.004 0.000 ARG O 42 *********************** 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 148 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7260 (m100) cc_final: 0.6757 (m100) REVERT: G 1272 ASP cc_start: 0.6420 (m-30) cc_final: 0.6167 (m-30) REVERT: G 1563 ARG cc_start: 0.6785 (mtm-85) cc_final: 0.6479 (mtt90) REVERT: G 1650 TRP cc_start: 0.5807 (OUTLIER) cc_final: 0.5600 (t60) REVERT: N 31 LYS cc_start: 0.8120 (mttp) cc_final: 0.7889 (mttm) REVERT: N 77 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8163 (mtmm) REVERT: O 38 ASN cc_start: 0.7827 (t0) cc_final: 0.7476 (t0) REVERT: O 41 GLU cc_start: 0.6385 (pm20) cc_final: 0.6113 (pm20) REVERT: O 99 ARG cc_start: 0.7749 (mmt-90) cc_final: 0.6981 (mtp85) REVERT: P 117 LYS cc_start: 0.7986 (tttm) cc_final: 0.7655 (tttm) REVERT: Q 56 LYS cc_start: 0.7464 (ptmt) cc_final: 0.7215 (ptmm) REVERT: R 57 VAL cc_start: 0.7717 (t) cc_final: 0.7390 (m) REVERT: R 77 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7412 (mttm) outliers start: 19 outliers final: 15 residues processed: 142 average time/residue: 0.3284 time to fit residues: 63.3189 Evaluate side-chains 141 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 1650 TRP Chi-restraints excluded: chain G residue 1653 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 25 ASN Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1191 HIS G1207 GLN N 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12972 Z= 0.221 Angle : 0.778 31.558 18432 Z= 0.375 Chirality : 0.037 0.194 2078 Planarity : 0.004 0.039 1571 Dihedral : 28.636 111.270 3441 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 946 helix: 0.99 (0.21), residues: 595 sheet: -0.57 (0.75), residues: 55 loop : -0.36 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 PHE 0.016 0.002 PHE Q 67 TYR 0.044 0.002 TYR N 88 ARG 0.004 0.000 ARG O 42 *********************** 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 144 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: G 1016 GLU cc_start: 0.7379 (tp30) cc_final: 0.7074 (tp30) REVERT: G 1021 TRP cc_start: 0.7222 (m100) cc_final: 0.6738 (m100) REVERT: G 1563 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6404 (mtt90) REVERT: N 31 LYS cc_start: 0.8128 (mttp) cc_final: 0.7894 (mttm) REVERT: N 77 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8169 (mtmm) REVERT: O 38 ASN cc_start: 0.7810 (t0) cc_final: 0.7471 (t0) REVERT: O 99 ARG cc_start: 0.7761 (mmt-90) cc_final: 0.7003 (mtp180) REVERT: P 117 LYS cc_start: 0.8038 (tttm) cc_final: 0.7719 (ttmm) REVERT: Q 56 LYS cc_start: 0.7506 (ptmt) cc_final: 0.7265 (ptmm) REVERT: R 57 VAL cc_start: 0.7720 (t) cc_final: 0.7393 (m) REVERT: R 77 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7412 (mttm) outliers start: 17 outliers final: 14 residues processed: 139 average time/residue: 0.3153 time to fit residues: 58.7086 Evaluate side-chains 139 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 1653 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 25 ASN Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1191 HIS ** G1207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12972 Z= 0.207 Angle : 0.769 31.102 18432 Z= 0.370 Chirality : 0.036 0.186 2078 Planarity : 0.004 0.039 1571 Dihedral : 28.549 111.644 3441 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.79 % Allowed : 15.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 946 helix: 1.09 (0.21), residues: 596 sheet: -0.07 (0.79), residues: 49 loop : -0.38 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G1650 HIS 0.005 0.001 HIS G1080 PHE 0.014 0.001 PHE Q 67 TYR 0.047 0.002 TYR N 88 ARG 0.004 0.000 ARG O 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: G 1016 GLU cc_start: 0.7385 (tp30) cc_final: 0.7064 (tp30) REVERT: G 1021 TRP cc_start: 0.7156 (m100) cc_final: 0.6740 (m100) REVERT: G 1563 ARG cc_start: 0.6708 (mtm-85) cc_final: 0.6356 (mtt90) REVERT: N 77 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8124 (mtmm) REVERT: O 38 ASN cc_start: 0.7846 (t0) cc_final: 0.7492 (t0) REVERT: O 99 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.6997 (mtp180) REVERT: Q 56 LYS cc_start: 0.7479 (ptmt) cc_final: 0.7227 (ptmm) REVERT: R 57 VAL cc_start: 0.7700 (t) cc_final: 0.7389 (m) REVERT: R 77 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7417 (mttm) outliers start: 15 outliers final: 15 residues processed: 136 average time/residue: 0.3142 time to fit residues: 57.9907 Evaluate side-chains 138 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 M residue 117 VAL 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 Q residue 80 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 25 ASN Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117274 restraints weight = 17463.185| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 0.97 r_work: 0.3441 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12972 Z= 0.200 Angle : 0.762 30.909 18432 Z= 0.365 Chirality : 0.036 0.180 2078 Planarity : 0.004 0.039 1571 Dihedral : 28.471 109.918 3441 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.79 % Allowed : 15.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.27), residues: 946 helix: 1.18 (0.21), residues: 596 sheet: -0.03 (0.79), residues: 49 loop : -0.41 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G1650 HIS 0.005 0.001 HIS G1080 PHE 0.022 0.002 PHE G1264 TYR 0.043 0.002 TYR N 88 ARG 0.003 0.000 ARG G1661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2652.07 seconds wall clock time: 47 minutes 46.36 seconds (2866.36 seconds total)