Starting phenix.real_space_refine on Sat Dec 9 20:49:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/12_2023/8oos_17027_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/12_2023/8oos_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_17027/12_2023/8oos_17027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/12_2023/8oos_17027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/12_2023/8oos_17027_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oos_17027/12_2023/8oos_17027_updated.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.46, per 1000 atoms: 0.61 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: 6.11 Conformation dependent library (CDL) restraints added in 1.4 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... running ksdssp... Secondary structure from input PDB file: 45 helices and 2 sheets defined 56.6% alpha, 4.0% beta 67 base pairs and 187 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'G' and resid 966 through 968 No H-bonds generated for 'chain 'G' and resid 966 through 968' Processing helix chain 'G' and resid 974 through 988 Processing helix chain 'G' and resid 1003 through 1018 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 1030 through 1043 removed outlier: 4.544A pdb=" N HIS G1034 " --> pdb=" O SER G1031 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP G1036 " --> pdb=" O LEU G1033 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN G1037 " --> pdb=" O HIS G1034 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G1038 " --> pdb=" O ASN G1035 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL G1040 " --> pdb=" O GLN G1037 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE G1043 " --> pdb=" O VAL G1040 " (cutoff:3.500A) Processing helix chain 'G' and resid 1056 through 1065 removed outlier: 3.794A pdb=" N LYS G1064 " --> pdb=" O LYS G1060 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE G1065 " --> pdb=" O VAL G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1088 through 1091 No H-bonds generated for 'chain 'G' and resid 1088 through 1091' Processing helix chain 'G' and resid 1093 through 1096 No H-bonds generated for 'chain 'G' and resid 1093 through 1096' Processing helix chain 'G' and resid 1109 through 1112 Processing helix chain 'G' and resid 1118 through 1125 removed outlier: 3.684A pdb=" N LEU G1123 " --> pdb=" O ARG G1119 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY G1125 " --> pdb=" O LYS G1121 " (cutoff:3.500A) Processing helix chain 'G' and resid 1144 through 1153 removed outlier: 4.345A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1190 through 1193 No H-bonds generated for 'chain 'G' and resid 1190 through 1193' Processing helix chain 'G' and resid 1224 through 1239 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 1269 removed outlier: 4.968A pdb=" N MET G1262 " --> pdb=" O MET G1258 " (cutoff:3.500A) Processing helix chain 'G' and resid 1271 through 1273 No H-bonds generated for 'chain 'G' and resid 1271 through 1273' Processing helix chain 'G' and resid 1545 through 1550 Processing helix chain 'G' and resid 1553 through 1568 Processing helix chain 'G' and resid 1579 through 1590 Processing helix chain 'G' and resid 1605 through 1617 Processing helix chain 'G' and resid 1652 through 1662 removed outlier: 3.911A pdb=" N ALA G1662 " --> pdb=" O ALA G1658 " (cutoff:3.500A) Processing helix chain 'G' and resid 1682 through 1700 Processing helix chain 'M' and resid 64 through 77 removed outlier: 4.228A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 113 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 121 through 131 Processing helix chain 'N' and resid 25 through 28 Processing helix chain 'N' and resid 31 through 40 Processing helix chain 'N' and resid 50 through 76 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 83 through 92 Processing helix chain 'O' and resid 17 through 21 Processing helix chain 'O' and resid 27 through 36 Processing helix chain 'O' and resid 47 through 72 Processing helix chain 'O' and resid 80 through 89 Processing helix chain 'O' and resid 91 through 96 Processing helix chain 'O' and resid 113 through 115 No H-bonds generated for 'chain 'O' and resid 113 through 115' Processing helix chain 'P' and resid 35 through 45 removed outlier: 3.849A pdb=" N GLN P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 81 Processing helix chain 'P' and resid 88 through 98 Processing helix chain 'P' and resid 101 through 118 Processing helix chain 'Q' and resid 45 through 54 Processing helix chain 'Q' and resid 64 through 76 Processing helix chain 'Q' and resid 86 through 113 removed outlier: 3.695A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 131 Processing helix chain 'R' and resid 25 through 28 Processing helix chain 'R' and resid 31 through 40 Processing helix chain 'R' and resid 50 through 75 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 83 through 93 Processing sheet with id= A, first strand: chain 'G' and resid 993 through 995 removed outlier: 3.905A pdb=" N GLY G 993 " --> pdb=" O ARG G1131 " (cutoff:3.500A) 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: 4.590A pdb=" N SER G1085 " --> pdb=" O TYR G1052 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 1214 through 1217 374 hydrogen bonds defined for protein. 1098 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: 5.05 Time building geometry restraints manager: 6.48 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: 8187 3.09 - 3.69: 20015 3.69 - 4.30: 31699 4.30 - 4.90: 47258 Nonbonded interactions: 107193 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 107188 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: 2.430 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: 12.740 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 40.780 Find NCS groups from input model: 0.320 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.180 ------------------------------------------------------------------------------- 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= 0.371 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 : 1.066 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3807 time to fit residues: 105.8652 Evaluate side-chains 151 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2491 ------------------------------------------------------------------------------- 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: 1.9990 chunk 86 optimal weight: 0.0060 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 P 60 ASN R 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12972 Z= 0.192 Angle : 0.784 29.323 18432 Z= 0.387 Chirality : 0.038 0.170 2078 Planarity : 0.004 0.031 1571 Dihedral : 29.026 122.193 3441 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.83 % Allowed : 6.32 % Favored : 92.85 % 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: 0.24 (0.27), residues: 946 helix: 0.41 (0.21), residues: 585 sheet: 0.58 (0.81), residues: 42 loop : -0.10 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G1650 HIS 0.003 0.001 HIS G1663 PHE 0.013 0.002 PHE G1096 TYR 0.015 0.002 TYR O 50 ARG 0.005 0.001 ARG G1661 *********************** 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 164 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 1.076 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 161 average time/residue: 0.3367 time to fit residues: 71.3387 Evaluate side-chains 135 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1102 time to fit residues: 2.0322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 70 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1037 GLN P 44 GLN P 60 ASN P 81 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12972 Z= 0.193 Angle : 0.759 29.846 18432 Z= 0.370 Chirality : 0.036 0.176 2078 Planarity : 0.004 0.033 1571 Dihedral : 28.704 109.029 3441 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.67 % Allowed : 8.94 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.28), residues: 946 helix: 0.88 (0.21), residues: 585 sheet: 0.15 (0.77), residues: 47 loop : 0.06 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G1650 HIS 0.007 0.001 HIS G1080 PHE 0.016 0.002 PHE P 67 TYR 0.018 0.001 TYR N 88 ARG 0.006 0.001 ARG O 42 *********************** 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 154 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.037 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 148 average time/residue: 0.3120 time to fit residues: 62.6531 Evaluate side-chains 134 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1638 time to fit residues: 2.9651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.0050 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 60 ASN ** 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: 0.6909 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12972 Z= 0.171 Angle : 0.736 30.074 18432 Z= 0.355 Chirality : 0.035 0.161 2078 Planarity : 0.004 0.032 1571 Dihedral : 28.399 108.509 3441 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.83 % Allowed : 10.61 % Favored : 88.56 % 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: 1.12 (0.28), residues: 946 helix: 1.18 (0.21), residues: 586 sheet: 0.60 (0.69), residues: 57 loop : 0.08 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1650 HIS 0.004 0.001 HIS G1080 PHE 0.016 0.001 PHE P 67 TYR 0.025 0.001 TYR N 88 ARG 0.005 0.000 ARG O 20 *********************** 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 140 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 1.037 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 136 average time/residue: 0.3162 time to fit residues: 58.3271 Evaluate side-chains 126 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1102 time to fit residues: 2.1723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1037 GLN N 27 GLN P 79 HIS ** 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: 0.6947 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12972 Z= 0.199 Angle : 0.753 29.949 18432 Z= 0.364 Chirality : 0.035 0.187 2078 Planarity : 0.004 0.033 1571 Dihedral : 28.506 103.476 3441 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.19 % Allowed : 11.56 % Favored : 87.25 % 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: 1.09 (0.27), residues: 946 helix: 1.17 (0.21), residues: 577 sheet: 0.71 (0.72), residues: 57 loop : 0.06 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1650 HIS 0.006 0.001 HIS P 79 PHE 0.016 0.002 PHE P 67 TYR 0.021 0.002 TYR N 88 ARG 0.005 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 139 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.131 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 134 average time/residue: 0.3133 time to fit residues: 57.2111 Evaluate side-chains 130 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1259 time to fit residues: 2.8829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 0.0670 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1207 GLN G1663 HIS ** G1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12972 Z= 0.199 Angle : 0.750 29.970 18432 Z= 0.359 Chirality : 0.035 0.176 2078 Planarity : 0.004 0.033 1571 Dihedral : 28.416 102.257 3441 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.60 % Allowed : 12.75 % Favored : 86.65 % 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: 1.08 (0.27), residues: 946 helix: 1.19 (0.21), residues: 577 sheet: 0.74 (0.72), residues: 57 loop : -0.01 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1650 HIS 0.003 0.001 HIS N 75 PHE 0.012 0.001 PHE G1079 TYR 0.019 0.002 TYR N 88 ARG 0.006 0.000 ARG R 78 *********************** 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 134 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 134 average time/residue: 0.3063 time to fit residues: 56.1797 Evaluate side-chains 121 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0020 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1207 GLN ** G1663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1667 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4145 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 : 0.752 29.952 18432 Z= 0.361 Chirality : 0.035 0.178 2078 Planarity : 0.004 0.034 1571 Dihedral : 28.491 101.348 3441 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.60 % Allowed : 13.71 % Favored : 85.70 % 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: 0.98 (0.27), residues: 946 helix: 1.13 (0.21), residues: 578 sheet: 0.74 (0.72), residues: 52 loop : -0.10 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1650 HIS 0.005 0.001 HIS G1663 PHE 0.017 0.002 PHE G1264 TYR 0.015 0.002 TYR N 88 ARG 0.005 0.000 ARG R 78 *********************** 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 129 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 0.991 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 126 average time/residue: 0.3016 time to fit residues: 52.3734 Evaluate side-chains 123 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1169 time to fit residues: 1.9763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1207 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: 0.6935 moved from start: 0.4266 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= 0.186 Angle : 0.743 30.071 18432 Z= 0.355 Chirality : 0.034 0.172 2078 Planarity : 0.004 0.034 1571 Dihedral : 28.396 102.119 3441 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.36 % Allowed : 14.06 % Favored : 85.58 % 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 (0.27), residues: 946 helix: 1.20 (0.21), residues: 578 sheet: 0.70 (0.72), residues: 52 loop : -0.08 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1650 HIS 0.002 0.001 HIS N 75 PHE 0.011 0.001 PHE Q 67 TYR 0.021 0.002 TYR N 88 ARG 0.004 0.000 ARG R 78 *********************** 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 128 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 127 average time/residue: 0.2993 time to fit residues: 52.5124 Evaluate side-chains 122 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1324 time to fit residues: 1.7691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1207 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: 0.6971 moved from start: 0.4304 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= 0.232 Angle : 0.772 30.358 18432 Z= 0.372 Chirality : 0.036 0.213 2078 Planarity : 0.004 0.033 1571 Dihedral : 28.651 101.494 3441 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.24 % Allowed : 14.54 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 586 sheet: 0.38 (0.70), residues: 47 loop : -0.36 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1036 HIS 0.004 0.001 HIS N 75 PHE 0.017 0.002 PHE G1079 TYR 0.016 0.002 TYR O 50 ARG 0.004 0.000 ARG R 78 *********************** 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 124 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.116 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.3032 time to fit residues: 51.7342 Evaluate side-chains 120 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1135 time to fit residues: 1.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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: 0.6931 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12972 Z= 0.178 Angle : 0.745 29.899 18432 Z= 0.354 Chirality : 0.034 0.174 2078 Planarity : 0.004 0.035 1571 Dihedral : 28.387 105.159 3441 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.27), residues: 946 helix: 1.19 (0.22), residues: 584 sheet: 0.47 (0.71), residues: 47 loop : -0.30 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G1021 HIS 0.003 0.001 HIS N 75 PHE 0.011 0.001 PHE G1264 TYR 0.016 0.001 TYR N 88 ARG 0.004 0.000 ARG O 20 ********************** 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 121 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2935 time to fit residues: 49.1485 Evaluate side-chains 119 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 0.0670 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 0.0570 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117531 restraints weight = 17395.956| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 0.93 r_work: 0.3459 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12972 Z= 0.173 Angle : 0.740 30.068 18432 Z= 0.350 Chirality : 0.034 0.168 2078 Planarity : 0.004 0.035 1571 Dihedral : 28.202 104.500 3441 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 14.66 % Favored : 85.34 % 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: 1.04 (0.27), residues: 946 helix: 1.31 (0.22), residues: 585 sheet: 0.51 (0.72), residues: 47 loop : -0.35 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G1650 HIS 0.003 0.001 HIS N 75 PHE 0.014 0.001 PHE G1264 TYR 0.015 0.001 TYR G 975 ARG 0.004 0.000 ARG O 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.44 seconds wall clock time: 49 minutes 13.16 seconds (2953.16 seconds total)