Starting phenix.real_space_refine on Sat Jul 20 22:07:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/07_2024/8oos_17027_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/07_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_17027/07_2024/8oos_17027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/07_2024/8oos_17027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/07_2024/8oos_17027_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/07_2024/8oos_17027_neut.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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 8.10, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 6.43 Conformation dependent library (CDL) restraints added in 1.5 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: 5.37 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: 5.79 Time building geometry restraints manager: 6.91 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: 89.55 - 107.61: 2041 107.61 - 125.67: 15642 125.67 - 143.74: 747 143.74 - 161.80: 0 161.80 - 179.87: 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 2.520 nonbonded pdb=" OD1 ASP G1559 " pdb=" OH TYR G1588 " model vdw 2.189 2.440 nonbonded pdb=" OH TYR M 99 " pdb=" OE1 GLU M 133 " model vdw 2.228 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'N' and resid 23 through 93) selection = (chain 'R' and resid 23 through 93) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 43.500 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.270 ------------------------------------------------------------------------------- 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 : 1.031 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: 0.3757 time to fit residues: 103.9698 Evaluate side-chains 153 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.7980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1087 GLN G1141 ASN G1186 GLN M 68 GLN P 60 ASN P 81 ASN Q 113 HIS R 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12972 Z= 0.241 Angle : 0.824 30.933 18432 Z= 0.410 Chirality : 0.040 0.169 2078 Planarity : 0.005 0.037 1571 Dihedral : 29.178 119.696 3441 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.07 % Allowed : 7.27 % Favored : 91.66 % 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: 0.01 (0.27), residues: 946 helix: 0.11 (0.20), residues: 587 sheet: 0.91 (0.86), residues: 42 loop : -0.01 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G1650 HIS 0.004 0.001 HIS N 75 PHE 0.014 0.002 PHE G1079 TYR 0.019 0.002 TYR O 50 ARG 0.005 0.001 ARG G1698 *********************** 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 157 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 1001 LEU cc_start: 0.7301 (mt) cc_final: 0.7097 (mt) REVERT: G 1021 TRP cc_start: 0.7025 (m100) cc_final: 0.6724 (m100) REVERT: G 1186 GLN cc_start: 0.3918 (OUTLIER) cc_final: 0.2751 (tt0) REVERT: G 1262 MET cc_start: 0.5087 (tpp) cc_final: 0.4879 (tpp) REVERT: G 1585 MET cc_start: 0.7010 (tpt) cc_final: 0.6733 (tpp) REVERT: O 38 ASN cc_start: 0.7753 (t0) cc_final: 0.7508 (t0) REVERT: P 40 LYS cc_start: 0.7799 (mttt) cc_final: 0.7571 (mttp) REVERT: Q 49 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7374 (ttm110) REVERT: R 57 VAL cc_start: 0.7680 (t) cc_final: 0.7349 (m) REVERT: R 77 LYS cc_start: 0.7805 (mtmt) cc_final: 0.7386 (mttt) REVERT: R 95 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7487 (mtp85) outliers start: 9 outliers final: 7 residues processed: 156 average time/residue: 0.3625 time to fit residues: 73.3175 Evaluate side-chains 142 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3231 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= 0.219 Angle : 0.786 30.190 18432 Z= 0.383 Chirality : 0.038 0.185 2078 Planarity : 0.004 0.034 1571 Dihedral : 28.823 116.170 3441 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.67 % Allowed : 9.65 % Favored : 88.68 % 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: 0.67 (0.27), residues: 946 helix: 0.76 (0.21), residues: 586 sheet: 0.34 (0.84), residues: 47 loop : 0.10 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G1650 HIS 0.005 0.001 HIS P 79 PHE 0.015 0.002 PHE P 67 TYR 0.035 0.002 TYR N 88 ARG 0.004 0.001 ARG G1234 *********************** 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: 14 poor density : 139 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.6977 (m100) cc_final: 0.6728 (m100) REVERT: G 1230 TYR cc_start: 0.5074 (t80) cc_final: 0.4078 (t80) REVERT: G 1262 MET cc_start: 0.5113 (tpp) cc_final: 0.4911 (tpp) REVERT: G 1585 MET cc_start: 0.6987 (tpt) cc_final: 0.6734 (tpp) REVERT: G 1650 TRP cc_start: 0.5584 (OUTLIER) cc_final: 0.5290 (t60) REVERT: N 25 ASN cc_start: 0.6924 (m-40) cc_final: 0.6444 (m-40) REVERT: O 38 ASN cc_start: 0.7808 (t0) cc_final: 0.7542 (t0) REVERT: P 117 LYS cc_start: 0.7883 (tttm) cc_final: 0.7584 (ttmm) REVERT: R 57 VAL cc_start: 0.7718 (t) cc_final: 0.7419 (m) REVERT: R 77 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7416 (mttt) REVERT: R 95 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7397 (mtp85) outliers start: 14 outliers final: 9 residues processed: 149 average time/residue: 0.3426 time to fit residues: 67.5199 Evaluate side-chains 140 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 1620 GLU Chi-restraints excluded: chain G residue 1635 ILE Chi-restraints excluded: chain G residue 1650 TRP Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1186 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12972 Z= 0.217 Angle : 0.772 30.352 18432 Z= 0.376 Chirality : 0.037 0.174 2078 Planarity : 0.004 0.035 1571 Dihedral : 28.670 116.203 3441 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.50 % Allowed : 11.08 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.27), residues: 946 helix: 0.94 (0.21), residues: 592 sheet: 0.36 (0.84), residues: 47 loop : -0.04 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G1650 HIS 0.005 0.001 HIS P 79 PHE 0.020 0.002 PHE G1264 TYR 0.042 0.002 TYR N 88 ARG 0.005 0.000 ARG O 42 *********************** 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 157 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: G 1021 TRP cc_start: 0.7092 (m100) cc_final: 0.6837 (m100) REVERT: G 1262 MET cc_start: 0.5165 (tpp) cc_final: 0.4932 (tpp) REVERT: G 1264 PHE cc_start: 0.6084 (m-80) cc_final: 0.5737 (m-80) REVERT: G 1585 MET cc_start: 0.7060 (tpt) cc_final: 0.6729 (tpp) REVERT: G 1650 TRP cc_start: 0.5647 (OUTLIER) cc_final: 0.5389 (t60) REVERT: N 25 ASN cc_start: 0.6975 (m-40) cc_final: 0.6581 (m-40) REVERT: O 38 ASN cc_start: 0.7825 (t0) cc_final: 0.7576 (t0) REVERT: P 80 TYR cc_start: 0.6689 (m-80) cc_final: 0.6408 (m-80) REVERT: P 110 GLU cc_start: 0.7845 (tp30) cc_final: 0.7619 (tp30) REVERT: P 117 LYS cc_start: 0.7896 (tttm) cc_final: 0.7607 (ttmm) REVERT: R 57 VAL cc_start: 0.7722 (t) cc_final: 0.7421 (m) REVERT: R 77 LYS cc_start: 0.7828 (mtmt) cc_final: 0.7429 (mttm) REVERT: R 95 ARG cc_start: 0.7729 (mtt90) cc_final: 0.7338 (mtp85) outliers start: 21 outliers final: 13 residues processed: 153 average time/residue: 0.3259 time to fit residues: 66.2549 Evaluate side-chains 143 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1620 GLU 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 M residue 117 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 70 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: 1.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 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: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1035 ASN G1235 ASN P 60 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3830 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= 0.208 Angle : 0.762 30.172 18432 Z= 0.368 Chirality : 0.036 0.173 2078 Planarity : 0.004 0.035 1571 Dihedral : 28.584 115.550 3441 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.50 % Allowed : 12.51 % Favored : 84.98 % 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: 1.05 (0.28), residues: 946 helix: 1.16 (0.21), residues: 587 sheet: 0.52 (0.73), residues: 57 loop : -0.01 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 PHE 0.014 0.002 PHE Q 67 TYR 0.046 0.002 TYR N 88 ARG 0.004 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 153 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.069 Fit side-chains REVERT: G 1021 TRP cc_start: 0.7085 (m100) cc_final: 0.6873 (m100) REVERT: G 1262 MET cc_start: 0.5117 (tpp) cc_final: 0.4883 (tpp) REVERT: G 1264 PHE cc_start: 0.6021 (m-80) cc_final: 0.5747 (m-80) REVERT: G 1585 MET cc_start: 0.7008 (tpt) cc_final: 0.6727 (tpp) REVERT: G 1650 TRP cc_start: 0.5683 (OUTLIER) cc_final: 0.5380 (t60) REVERT: N 25 ASN cc_start: 0.6961 (m-40) cc_final: 0.6606 (m-40) REVERT: O 38 ASN cc_start: 0.7831 (t0) cc_final: 0.7333 (t0) REVERT: P 110 GLU cc_start: 0.7806 (tp30) cc_final: 0.7573 (tp30) REVERT: P 117 LYS cc_start: 0.7896 (tttm) cc_final: 0.7618 (ttmm) REVERT: R 57 VAL cc_start: 0.7694 (t) cc_final: 0.7397 (m) REVERT: R 77 LYS cc_start: 0.7859 (mtmt) cc_final: 0.7453 (mttm) outliers start: 21 outliers final: 15 residues processed: 148 average time/residue: 0.3207 time to fit residues: 63.1675 Evaluate side-chains 139 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 O residue 116 LEU Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 117 VAL 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 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1207 GLN G1235 ASN P 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12972 Z= 0.280 Angle : 0.809 30.562 18432 Z= 0.395 Chirality : 0.039 0.194 2078 Planarity : 0.005 0.040 1571 Dihedral : 28.943 114.934 3441 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.74 % Allowed : 13.35 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.21), residues: 593 sheet: 0.55 (0.73), residues: 57 loop : -0.28 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G1650 HIS 0.006 0.001 HIS P 79 PHE 0.021 0.002 PHE G1079 TYR 0.050 0.002 TYR N 88 ARG 0.008 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 150 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: G 1018 TYR cc_start: 0.7253 (m-10) cc_final: 0.6885 (m-10) REVERT: G 1186 GLN cc_start: 0.5548 (OUTLIER) cc_final: 0.4467 (pt0) REVERT: G 1264 PHE cc_start: 0.6034 (m-80) cc_final: 0.5543 (m-80) REVERT: G 1585 MET cc_start: 0.7023 (tpt) cc_final: 0.6768 (tpp) REVERT: N 25 ASN cc_start: 0.6941 (m-40) cc_final: 0.6462 (m110) REVERT: O 13 LYS cc_start: 0.5804 (tppt) cc_final: 0.5417 (tppt) REVERT: O 38 ASN cc_start: 0.7851 (t0) cc_final: 0.7595 (t0) REVERT: P 110 GLU cc_start: 0.7878 (tp30) cc_final: 0.7632 (tp30) REVERT: P 117 LYS cc_start: 0.7862 (tttm) cc_final: 0.7583 (ttmm) REVERT: R 57 VAL cc_start: 0.7734 (t) cc_final: 0.7400 (m) REVERT: R 77 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7433 (mttt) outliers start: 23 outliers final: 20 residues processed: 146 average time/residue: 0.3065 time to fit residues: 60.5288 Evaluate side-chains 142 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1190 LEU Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1620 GLU Chi-restraints excluded: chain G residue 1623 ILE Chi-restraints excluded: chain G residue 1639 THR 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 O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 95 VAL 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 50 ILE Chi-restraints excluded: chain R residue 70 VAL 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: 0.1980 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.0970 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1035 ASN G1151 HIS G1235 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12972 Z= 0.169 Angle : 0.743 29.941 18432 Z= 0.355 Chirality : 0.034 0.159 2078 Planarity : 0.004 0.037 1571 Dihedral : 28.393 114.828 3441 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.26 % Allowed : 14.06 % Favored : 83.67 % 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: 1.22 (0.28), residues: 946 helix: 1.30 (0.21), residues: 593 sheet: 0.74 (0.75), residues: 57 loop : -0.01 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1650 HIS 0.007 0.001 HIS G1151 PHE 0.013 0.001 PHE M 67 TYR 0.050 0.002 TYR N 88 ARG 0.005 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 153 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.053 Fit side-chains REVERT: G 1021 TRP cc_start: 0.7072 (m100) cc_final: 0.6844 (m100) REVERT: G 1264 PHE cc_start: 0.5966 (m-80) cc_final: 0.5729 (m-80) REVERT: G 1272 ASP cc_start: 0.6403 (m-30) cc_final: 0.6037 (m-30) REVERT: G 1545 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5891 (mmm) REVERT: G 1585 MET cc_start: 0.6985 (tpt) cc_final: 0.6716 (tpt) REVERT: G 1650 TRP cc_start: 0.5647 (OUTLIER) cc_final: 0.5230 (t60) REVERT: N 25 ASN cc_start: 0.6824 (m-40) cc_final: 0.6504 (m110) REVERT: O 13 LYS cc_start: 0.5823 (tppt) cc_final: 0.5453 (tppt) REVERT: O 38 ASN cc_start: 0.7851 (t0) cc_final: 0.7508 (t0) REVERT: O 99 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.6999 (mtp85) REVERT: P 110 GLU cc_start: 0.7765 (tp30) cc_final: 0.7529 (tp30) REVERT: P 117 LYS cc_start: 0.7940 (tttm) cc_final: 0.7617 (tttm) REVERT: R 57 VAL cc_start: 0.7709 (t) cc_final: 0.7414 (m) REVERT: R 77 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7446 (mttt) outliers start: 19 outliers final: 14 residues processed: 147 average time/residue: 0.3224 time to fit residues: 63.4952 Evaluate side-chains 140 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1623 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 O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 105 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 60 ASN R 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4208 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= 0.231 Angle : 0.774 30.319 18432 Z= 0.375 Chirality : 0.036 0.183 2078 Planarity : 0.004 0.036 1571 Dihedral : 28.642 111.980 3441 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.74 % Allowed : 14.06 % Favored : 83.19 % 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: 0.97 (0.27), residues: 946 helix: 1.13 (0.21), residues: 593 sheet: 0.62 (0.74), residues: 57 loop : -0.18 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G1650 HIS 0.004 0.001 HIS G1663 PHE 0.015 0.002 PHE Q 67 TYR 0.044 0.002 TYR N 88 ARG 0.005 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 155 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.029 Fit side-chains REVERT: G 1018 TYR cc_start: 0.7389 (m-10) cc_final: 0.6920 (m-10) REVERT: G 1230 TYR cc_start: 0.4833 (t80) cc_final: 0.4429 (t80) REVERT: G 1264 PHE cc_start: 0.6102 (m-80) cc_final: 0.5373 (m-80) REVERT: G 1272 ASP cc_start: 0.6401 (m-30) cc_final: 0.6029 (m-30) REVERT: N 25 ASN cc_start: 0.6864 (m-40) cc_final: 0.6437 (m110) REVERT: O 13 LYS cc_start: 0.5848 (tppt) cc_final: 0.5542 (tppt) REVERT: O 38 ASN cc_start: 0.7846 (t0) cc_final: 0.7327 (t0) REVERT: O 99 ARG cc_start: 0.7769 (mmt-90) cc_final: 0.7002 (mtp85) REVERT: P 110 GLU cc_start: 0.7817 (tp30) cc_final: 0.7563 (tp30) REVERT: P 117 LYS cc_start: 0.7940 (tttm) cc_final: 0.7649 (ttmm) REVERT: Q 56 LYS cc_start: 0.7361 (ptmt) cc_final: 0.7140 (ptmm) REVERT: R 57 VAL cc_start: 0.7755 (t) cc_final: 0.7434 (m) REVERT: R 77 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7460 (mttt) outliers start: 23 outliers final: 19 residues processed: 149 average time/residue: 0.2977 time to fit residues: 59.8365 Evaluate side-chains 145 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1620 GLU 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 G residue 1701 ILE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 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 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: 0.7980 chunk 102 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1235 ASN P 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4327 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= 0.204 Angle : 0.759 30.223 18432 Z= 0.365 Chirality : 0.035 0.173 2078 Planarity : 0.004 0.036 1571 Dihedral : 28.477 111.163 3441 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.50 % Allowed : 14.54 % 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: 1.03 (0.28), residues: 946 helix: 1.20 (0.21), residues: 593 sheet: -0.04 (0.70), residues: 65 loop : -0.06 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1650 HIS 0.010 0.001 HIS G1080 PHE 0.014 0.001 PHE Q 67 TYR 0.056 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 149 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.078 Fit side-chains REVERT: G 1018 TYR cc_start: 0.7418 (m-10) cc_final: 0.7004 (m-10) REVERT: G 1021 TRP cc_start: 0.7135 (m100) cc_final: 0.6731 (m100) REVERT: G 1230 TYR cc_start: 0.4906 (t80) cc_final: 0.4625 (t80) REVERT: G 1264 PHE cc_start: 0.6052 (m-80) cc_final: 0.5755 (m-80) REVERT: G 1545 MET cc_start: 0.6140 (OUTLIER) cc_final: 0.5872 (mmm) REVERT: G 1650 TRP cc_start: 0.5493 (OUTLIER) cc_final: 0.4877 (t60) REVERT: N 25 ASN cc_start: 0.6868 (m-40) cc_final: 0.6333 (m110) REVERT: O 38 ASN cc_start: 0.7834 (t0) cc_final: 0.7489 (t0) REVERT: O 99 ARG cc_start: 0.7759 (mmt-90) cc_final: 0.7001 (mtp85) REVERT: P 110 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7550 (tp30) REVERT: P 117 LYS cc_start: 0.7989 (tttm) cc_final: 0.7704 (ttmm) REVERT: Q 56 LYS cc_start: 0.7412 (ptmt) cc_final: 0.7194 (ptmm) REVERT: R 57 VAL cc_start: 0.7718 (t) cc_final: 0.7393 (m) REVERT: R 77 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7427 (mttt) outliers start: 21 outliers final: 16 residues processed: 141 average time/residue: 0.3034 time to fit residues: 57.9108 Evaluate side-chains 143 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1620 GLU 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 G residue 1669 LYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 110 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 0.0070 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 85 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12972 Z= 0.161 Angle : 0.735 29.871 18432 Z= 0.351 Chirality : 0.034 0.148 2078 Planarity : 0.004 0.038 1571 Dihedral : 28.192 109.847 3441 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 14.54 % Favored : 83.19 % 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: 1.35 (0.28), residues: 946 helix: 1.46 (0.21), residues: 593 sheet: 0.08 (0.71), residues: 65 loop : 0.05 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1650 HIS 0.006 0.001 HIS G1080 PHE 0.013 0.001 PHE M 67 TYR 0.057 0.002 TYR N 88 ARG 0.003 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 149 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.087 Fit side-chains REVERT: G 1018 TYR cc_start: 0.7447 (m-10) cc_final: 0.7068 (m-10) REVERT: G 1021 TRP cc_start: 0.7225 (m100) cc_final: 0.6745 (m100) REVERT: G 1230 TYR cc_start: 0.4856 (t80) cc_final: 0.4581 (t80) REVERT: G 1264 PHE cc_start: 0.6004 (m-80) cc_final: 0.5712 (m-80) REVERT: G 1545 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5938 (mmm) REVERT: G 1650 TRP cc_start: 0.5458 (OUTLIER) cc_final: 0.4863 (t60) REVERT: N 25 ASN cc_start: 0.6798 (m-40) cc_final: 0.6314 (m-40) REVERT: O 38 ASN cc_start: 0.7798 (t0) cc_final: 0.7452 (t0) REVERT: O 99 ARG cc_start: 0.7760 (mmt-90) cc_final: 0.7004 (mtp85) REVERT: P 110 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7518 (tp30) REVERT: P 117 LYS cc_start: 0.8000 (tttm) cc_final: 0.7674 (tttm) REVERT: R 57 VAL cc_start: 0.7660 (t) cc_final: 0.7364 (m) REVERT: R 77 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7451 (mttm) outliers start: 19 outliers final: 15 residues processed: 142 average time/residue: 0.3108 time to fit residues: 59.7771 Evaluate side-chains 140 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1044 VAL Chi-restraints excluded: chain G residue 1186 GLN Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1545 MET Chi-restraints excluded: chain G residue 1620 GLU Chi-restraints excluded: chain G residue 1623 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 19 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain P residue 80 TYR Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 110 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 0.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116058 restraints weight = 17574.775| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 0.98 r_work: 0.3430 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4439 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= 0.232 Angle : 0.776 30.640 18432 Z= 0.375 Chirality : 0.036 0.185 2078 Planarity : 0.004 0.037 1571 Dihedral : 28.510 107.495 3441 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.50 % Allowed : 15.14 % 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: 1.06 (0.28), residues: 946 helix: 1.23 (0.21), residues: 593 sheet: 0.44 (0.74), residues: 59 loop : -0.17 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G1650 HIS 0.005 0.001 HIS G1080 PHE 0.015 0.002 PHE Q 67 TYR 0.055 0.002 TYR N 88 ARG 0.005 0.001 ARG O 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2703.68 seconds wall clock time: 48 minutes 39.49 seconds (2919.49 seconds total)