Starting phenix.real_space_refine on Thu Jul 2 00:31:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oo9_17007/07_2026/8oo9_17007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oo9_17007/07_2026/8oo9_17007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oo9_17007/07_2026/8oo9_17007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oo9_17007/07_2026/8oo9_17007.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oo9_17007/07_2026/8oo9_17007.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oo9_17007/07_2026/8oo9_17007.cif" model { file = "/net/cci-nas-00/data/ceres_data/8oo9_17007/07_2026/8oo9_17007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oo9_17007/07_2026/8oo9_17007.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 44 5.49 5 Mg 1 5.21 5 S 24 5.16 5 C 2737 2.51 5 N 802 2.21 5 O 903 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4516 Number of models: 1 Model: "" Number of chains: 4 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: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "L" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 430 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} 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: 1.13, per 1000 atoms: 0.25 Number of scatterers: 4516 At special positions: 0 Unit cell: (78.09, 78.912, 83.022, 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 24 16.00 P 44 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 903 8.00 N 802 7.00 C 2737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 124.6 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 54.2% alpha, 10.9% beta 14 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'G' and resid 973 through 989 Processing helix chain 'G' and resid 1002 through 1019 removed outlier: 3.602A pdb=" N GLN G1006 " --> pdb=" O GLY G1002 " (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 1112 Processing helix chain 'G' and resid 1117 through 1125 Processing helix chain 'G' and resid 1142 through 1154 removed outlier: 3.658A pdb=" N LEU G1149 " --> pdb=" O GLU G1145 " (cutoff:3.500A) Processing helix chain 'G' and resid 1187 through 1194 removed outlier: 3.707A pdb=" N MET G1192 " --> pdb=" O LYS G1188 " (cutoff:3.500A) Processing helix chain 'G' and resid 1202 through 1207 Processing helix chain 'G' and resid 1223 through 1235 Processing helix chain 'G' and resid 1236 through 1239 Processing helix chain 'G' and resid 1257 through 1270 removed outlier: 3.740A pdb=" N MET G1262 " --> pdb=" O MET G1258 " (cutoff:3.500A) Processing helix chain 'G' and resid 1270 through 1275 removed outlier: 3.945A pdb=" N PHE G1274 " --> pdb=" O HIS G1270 " (cutoff:3.500A) Processing helix chain 'G' and resid 1544 through 1551 Processing helix chain 'G' and resid 1552 through 1568 removed outlier: 3.730A pdb=" N GLU G1567 " --> pdb=" O ARG G1563 " (cutoff:3.500A) Processing helix chain 'G' and resid 1578 through 1592 removed outlier: 3.737A pdb=" N ILE G1582 " --> pdb=" O MET G1578 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU G1586 " --> pdb=" O ILE G1582 " (cutoff:3.500A) Processing helix chain 'G' and resid 1604 through 1618 Processing helix chain 'G' and resid 1651 through 1660 Processing helix chain 'G' and resid 1681 through 1700 removed outlier: 3.866A pdb=" N ARG G1685 " --> pdb=" O THR G1681 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS G1693 " --> pdb=" O ARG G1689 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU G1694 " --> pdb=" O ALA G1690 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU G1695 " --> pdb=" O LEU G1691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 1049 through 1052 removed outlier: 4.751A pdb=" N SER G1085 " --> pdb=" O TYR G1052 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE G1024 " --> pdb=" O MET G1082 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N THR G1084 " --> pdb=" O PHE G1024 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL G1026 " --> pdb=" O THR G1084 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU G1025 " --> pdb=" O ILE G1105 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET G1104 " --> pdb=" O LEU G1132 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU G1134 " --> pdb=" O MET G1104 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU G1106 " --> pdb=" O LEU G1134 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY G 993 " --> pdb=" O ARG G1131 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G1133 " --> pdb=" O GLY G 993 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE G 994 " --> pdb=" O LEU G1199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 1100 through 1101 Processing sheet with id=AA3, first strand: chain 'G' and resid 1214 through 1220 removed outlier: 6.257A pdb=" N ILE G1214 " --> pdb=" O VAL G1673 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG G1675 " --> pdb=" O ILE G1214 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE G1216 " --> pdb=" O ARG G1675 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE G1677 " --> pdb=" O ILE G1216 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL G1218 " --> pdb=" O ILE G1677 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL G1643 " --> pdb=" O TYR G1674 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU G1676 " --> pdb=" O VAL G1643 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE G1645 " --> pdb=" O LEU G1676 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N THR G1678 " --> pdb=" O PHE G1645 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU G1573 " --> pdb=" O ILE G1644 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL G1572 " --> pdb=" O PHE G1624 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU G1626 " --> pdb=" O VAL G1572 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU G1574 " --> pdb=" O LEU G1626 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS G1597 " --> pdb=" O LEU G1625 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER G1627 " --> pdb=" O CYS G1597 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU G1599 " --> pdb=" O SER G1627 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 143 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 0.69 Time building geometry restraints manager: 0.45 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: 1330 1.34 - 1.46: 1151 1.46 - 1.58: 2088 1.58 - 1.70: 78 1.70 - 1.82: 46 Bond restraints: 4693 Sorted by residual: bond pdb=" C4' DG L -36 " pdb=" C3' DG L -36 " ideal model delta sigma weight residual 1.529 1.587 -0.058 1.00e-02 1.00e+04 3.42e+01 bond pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.685 1.795 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C3' DG K 27 " pdb=" C2' DG K 27 " ideal model delta sigma weight residual 1.516 1.559 -0.043 8.00e-03 1.56e+04 2.88e+01 bond pdb=" C2' DG L -36 " pdb=" C1' DG L -36 " ideal model delta sigma weight residual 1.518 1.467 0.051 1.00e-02 1.00e+04 2.59e+01 ... (remaining 4688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.01: 6506 14.01 - 28.02: 4 28.02 - 42.04: 0 42.04 - 56.05: 0 56.05 - 70.06: 2 Bond angle restraints: 6512 Sorted by residual: angle pdb=" F3 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 109.63 179.69 -70.06 3.00e+00 1.11e-01 5.45e+02 angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F2 ALF G2003 " ideal model delta sigma weight residual 108.68 178.52 -69.84 3.00e+00 1.11e-01 5.42e+02 angle pdb=" F1 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 109.02 88.48 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F4 ALF G2003 " ideal model delta sigma weight residual 110.21 90.04 20.17 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " pdb=" F3 ALF G2003 " ideal model delta sigma weight residual 109.59 89.92 19.67 3.00e+00 1.11e-01 4.30e+01 ... (remaining 6507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 2477 32.81 - 65.62: 214 65.62 - 98.43: 7 98.43 - 131.25: 2 131.25 - 164.06: 1 Dihedral angle restraints: 2701 sinusoidal: 1412 harmonic: 1289 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 300.00 135.94 164.06 1 2.00e+01 2.50e-03 4.71e+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 300.00 169.04 130.97 1 2.00e+01 2.50e-03 3.97e+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 53.46 -113.46 1 2.00e+01 2.50e-03 3.36e+01 ... (remaining 2698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 445 0.054 - 0.107: 231 0.107 - 0.160: 33 0.160 - 0.214: 8 0.214 - 0.267: 3 Chirality restraints: 720 Sorted by residual: chirality pdb=" CB ILE G1582 " pdb=" CA ILE G1582 " pdb=" CG1 ILE G1582 " pdb=" CG2 ILE G1582 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C3' DC L -20 " pdb=" C4' DC L -20 " pdb=" O3' DC L -20 " pdb=" C2' DC L -20 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C2' ADP G2001 " pdb=" C1' ADP G2001 " pdb=" C3' ADP G2001 " pdb=" O2' ADP G2001 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 717 not shown) Planarity restraints: 667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC K 33 " -0.071 2.00e-02 2.50e+03 3.63e-02 2.97e+01 pdb=" N1 DC K 33 " 0.077 2.00e-02 2.50e+03 pdb=" C2 DC K 33 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DC K 33 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DC K 33 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC K 33 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC K 33 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DC K 33 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC K 33 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC L -25 " 0.059 2.00e-02 2.50e+03 3.28e-02 2.43e+01 pdb=" N1 DC L -25 " -0.075 2.00e-02 2.50e+03 pdb=" C2 DC L -25 " -0.015 2.00e-02 2.50e+03 pdb=" O2 DC L -25 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DC L -25 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC L -25 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC L -25 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DC L -25 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC L -25 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC L -28 " 0.048 2.00e-02 2.50e+03 2.77e-02 1.73e+01 pdb=" N1 DC L -28 " -0.066 2.00e-02 2.50e+03 pdb=" C2 DC L -28 " -0.011 2.00e-02 2.50e+03 pdb=" O2 DC L -28 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DC L -28 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC L -28 " 0.006 2.00e-02 2.50e+03 pdb=" N4 DC L -28 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC L -28 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC L -28 " 0.002 2.00e-02 2.50e+03 ... (remaining 664 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 13 2.48 - 3.09: 3126 3.09 - 3.69: 7057 3.69 - 4.30: 11365 4.30 - 4.90: 17524 Nonbonded interactions: 39085 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 2.007 2.170 nonbonded pdb=" N2 DG K 40 " pdb=" O2 DC L -40 " model vdw 2.323 3.120 nonbonded pdb=" O TYR G 975 " pdb=" NH1 ARG G1201 " model vdw 2.327 3.120 nonbonded pdb=" NH2 ARG G1608 " pdb=" OP2 DC L -28 " model vdw 2.366 3.120 ... (remaining 39080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.350 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.830 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.013 0.534 4694 Z= 0.982 Angle : 1.703 70.061 6512 Z= 0.753 Chirality : 0.063 0.267 720 Planarity : 0.013 0.140 667 Dihedral : 20.609 164.056 1865 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.37), residues: 431 helix: -1.96 (0.28), residues: 215 sheet: -0.20 (0.76), residues: 54 loop : -0.88 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.004 ARG G1201 TYR 0.025 0.006 TYR G1588 PHE 0.039 0.005 PHE G1079 TRP 0.042 0.004 TRP G1650 HIS 0.011 0.002 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00980 / 0.60 ( 4693) covalent geometry : angle 1.70350 / 0.75 ( 6512) hydrogen bonds : bond 0.22094 / 14.82 ( 177) hydrogen bonds : angle 8.94698 / 6.34 ( 488) Misc. bond : bond 0.53368 / 28.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: G 1001 LEU cc_start: 0.8600 (mt) cc_final: 0.8312 (mm) REVERT: G 1020 ILE cc_start: 0.7443 (mm) cc_final: 0.7217 (mt) REVERT: G 1143 MET cc_start: 0.8052 (mmp) cc_final: 0.7527 (mmt) REVERT: G 1186 GLN cc_start: 0.5578 (pm20) cc_final: 0.5134 (tt0) REVERT: G 1224 TYR cc_start: 0.7796 (p90) cc_final: 0.7327 (p90) REVERT: G 1240 MET cc_start: 0.7127 (mmm) cc_final: 0.6864 (mmt) REVERT: G 1585 MET cc_start: 0.8656 (tpt) cc_final: 0.8376 (tpp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1039 time to fit residues: 14.1764 Evaluate side-chains 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.0040 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.108270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094441 restraints weight = 7669.538| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 0.86 r_work: 0.3341 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4694 Z= 0.180 Angle : 1.124 29.740 6512 Z= 0.488 Chirality : 0.047 0.201 720 Planarity : 0.006 0.078 667 Dihedral : 24.821 148.946 947 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.01 % Allowed : 7.81 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.39), residues: 431 helix: -0.83 (0.31), residues: 220 sheet: -0.26 (0.68), residues: 65 loop : -0.21 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G1201 TYR 0.011 0.002 TYR G1018 PHE 0.016 0.002 PHE G1615 TRP 0.014 0.002 TRP G1650 HIS 0.003 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 ( 4693) covalent geometry : angle 1.12386 / 0.49 ( 6512) hydrogen bonds : bond 0.06701 / 4.36 ( 177) hydrogen bonds : angle 5.78493 / 3.94 ( 488) Misc. bond : bond 0.00932 / 0.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: G 1020 ILE cc_start: 0.7479 (mm) cc_final: 0.7240 (mt) REVERT: G 1143 MET cc_start: 0.7745 (mmp) cc_final: 0.7542 (mmt) REVERT: G 1186 GLN cc_start: 0.5431 (pm20) cc_final: 0.4803 (pt0) REVERT: G 1224 TYR cc_start: 0.7783 (p90) cc_final: 0.7469 (p90) REVERT: G 1688 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6948 (tttp) outliers start: 4 outliers final: 3 residues processed: 70 average time/residue: 0.0621 time to fit residues: 5.4008 Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1688 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1663 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.106653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092860 restraints weight = 7580.280| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 0.86 r_work: 0.3312 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4694 Z= 0.195 Angle : 1.071 29.705 6512 Z= 0.455 Chirality : 0.043 0.138 720 Planarity : 0.005 0.056 667 Dihedral : 24.880 144.824 947 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.01 % Allowed : 10.33 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.40), residues: 431 helix: -0.56 (0.32), residues: 227 sheet: -0.19 (0.69), residues: 65 loop : -0.52 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G1201 TYR 0.011 0.002 TYR G 975 PHE 0.012 0.002 PHE G1264 TRP 0.011 0.002 TRP G1650 HIS 0.009 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 4693) covalent geometry : angle 1.07054 / 0.46 ( 6512) hydrogen bonds : bond 0.06095 / 4.00 ( 177) hydrogen bonds : angle 5.39499 / 3.65 ( 488) Misc. bond : bond 0.00394 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: G 1001 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8167 (mm) REVERT: G 1186 GLN cc_start: 0.5279 (pm20) cc_final: 0.4672 (pt0) REVERT: G 1224 TYR cc_start: 0.7789 (p90) cc_final: 0.7559 (p90) REVERT: G 1240 MET cc_start: 0.6281 (mmt) cc_final: 0.5840 (mpp) REVERT: G 1580 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.7103 (mtm-85) REVERT: G 1688 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6945 (tttp) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.0863 time to fit residues: 6.7286 Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1648 SER Chi-restraints excluded: chain G residue 1688 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.107312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093515 restraints weight = 7526.346| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 0.87 r_work: 0.3324 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4694 Z= 0.156 Angle : 1.036 29.815 6512 Z= 0.431 Chirality : 0.041 0.137 720 Planarity : 0.004 0.046 667 Dihedral : 24.995 138.501 947 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.01 % Allowed : 11.84 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.40), residues: 431 helix: -0.25 (0.33), residues: 224 sheet: -0.21 (0.66), residues: 67 loop : -0.61 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G1201 TYR 0.013 0.001 TYR G1591 PHE 0.010 0.002 PHE G1264 TRP 0.009 0.002 TRP G1053 HIS 0.002 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 4693) covalent geometry : angle 1.03641 / 0.43 ( 6512) hydrogen bonds : bond 0.04946 / 3.24 ( 177) hydrogen bonds : angle 5.10504 / 3.43 ( 488) Misc. bond : bond 0.00094 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: G 1224 TYR cc_start: 0.7948 (p90) cc_final: 0.7736 (p90) REVERT: G 1240 MET cc_start: 0.6558 (mmt) cc_final: 0.6081 (mpp) REVERT: G 1580 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7063 (mtm180) REVERT: G 1688 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6990 (tttp) outliers start: 4 outliers final: 2 residues processed: 68 average time/residue: 0.0954 time to fit residues: 7.9666 Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1688 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 14 optimal weight: 0.0470 chunk 29 optimal weight: 0.0970 chunk 2 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1035 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094102 restraints weight = 7596.070| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 0.87 r_work: 0.3341 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4694 Z= 0.130 Angle : 1.023 29.587 6512 Z= 0.423 Chirality : 0.039 0.133 720 Planarity : 0.004 0.036 667 Dihedral : 24.750 131.878 947 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.26 % Allowed : 13.10 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.40), residues: 431 helix: -0.13 (0.34), residues: 224 sheet: -0.11 (0.67), residues: 67 loop : -0.62 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G1679 TYR 0.010 0.001 TYR G1018 PHE 0.007 0.001 PHE G1264 TRP 0.006 0.001 TRP G1650 HIS 0.003 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 4693) covalent geometry : angle 1.02300 / 0.42 ( 6512) hydrogen bonds : bond 0.04596 / 2.98 ( 177) hydrogen bonds : angle 4.95949 / 3.31 ( 488) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: G 1240 MET cc_start: 0.6562 (mmt) cc_final: 0.6079 (mpp) REVERT: G 1580 ARG cc_start: 0.7268 (mtm-85) cc_final: 0.7011 (mtm180) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.0924 time to fit residues: 7.1878 Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.092969 restraints weight = 7695.250| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 0.89 r_work: 0.3322 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4694 Z= 0.152 Angle : 1.029 29.627 6512 Z= 0.423 Chirality : 0.039 0.142 720 Planarity : 0.004 0.035 667 Dihedral : 24.689 124.695 947 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.01 % Allowed : 14.11 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.41), residues: 431 helix: -0.08 (0.34), residues: 227 sheet: -0.24 (0.66), residues: 67 loop : -0.67 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G1679 TYR 0.014 0.001 TYR G1224 PHE 0.009 0.001 PHE G1079 TRP 0.008 0.002 TRP G1650 HIS 0.003 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 4693) covalent geometry : angle 1.02864 / 0.42 ( 6512) hydrogen bonds : bond 0.04769 / 3.08 ( 177) hydrogen bonds : angle 4.91094 / 3.28 ( 488) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7651 (mpp) cc_final: 0.7059 (mpp) REVERT: G 1240 MET cc_start: 0.6707 (mmt) cc_final: 0.6254 (mpp) REVERT: G 1580 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.7041 (mtm180) outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.0824 time to fit residues: 6.2593 Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1210 LEU Chi-restraints excluded: chain G residue 1648 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1097 GLN G1636 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092187 restraints weight = 7604.131| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 0.89 r_work: 0.3299 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4694 Z= 0.181 Angle : 1.046 29.985 6512 Z= 0.434 Chirality : 0.040 0.183 720 Planarity : 0.004 0.034 667 Dihedral : 24.760 120.354 947 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.76 % Allowed : 13.85 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.40), residues: 431 helix: -0.21 (0.33), residues: 227 sheet: -0.41 (0.65), residues: 67 loop : -0.68 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G1679 TYR 0.019 0.002 TYR G1591 PHE 0.012 0.002 PHE G1079 TRP 0.009 0.002 TRP G1650 HIS 0.002 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 4693) covalent geometry : angle 1.04608 / 0.43 ( 6512) hydrogen bonds : bond 0.04939 / 3.19 ( 177) hydrogen bonds : angle 4.93330 / 3.30 ( 488) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7685 (mpp) cc_final: 0.7136 (mpt) REVERT: G 1001 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8246 (mm) REVERT: G 1240 MET cc_start: 0.6774 (mmt) cc_final: 0.6387 (mpp) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.0871 time to fit residues: 6.5131 Evaluate side-chains 59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1210 LEU Chi-restraints excluded: chain G residue 1648 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1097 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093155 restraints weight = 7665.596| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 0.89 r_work: 0.3320 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4694 Z= 0.146 Angle : 1.021 29.701 6512 Z= 0.418 Chirality : 0.039 0.188 720 Planarity : 0.004 0.034 667 Dihedral : 24.661 117.870 947 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 14.61 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.41), residues: 431 helix: -0.13 (0.34), residues: 228 sheet: -0.35 (0.66), residues: 67 loop : -0.68 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1201 TYR 0.015 0.001 TYR G1591 PHE 0.009 0.001 PHE G1548 TRP 0.009 0.002 TRP G1650 HIS 0.002 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 4693) covalent geometry : angle 1.02076 / 0.42 ( 6512) hydrogen bonds : bond 0.04443 / 2.86 ( 177) hydrogen bonds : angle 4.83436 / 3.23 ( 488) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7636 (mpp) cc_final: 0.7084 (mpt) REVERT: G 1001 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8164 (mm) REVERT: G 1240 MET cc_start: 0.6891 (mmt) cc_final: 0.6534 (mpp) outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.0893 time to fit residues: 6.5608 Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1210 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.0470 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1097 GLN G1692 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093657 restraints weight = 7558.607| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 0.89 r_work: 0.3330 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4694 Z= 0.136 Angle : 1.018 29.711 6512 Z= 0.416 Chirality : 0.038 0.162 720 Planarity : 0.004 0.040 667 Dihedral : 24.435 115.131 947 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.76 % Allowed : 14.36 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.41), residues: 431 helix: -0.01 (0.34), residues: 227 sheet: -0.33 (0.66), residues: 67 loop : -0.81 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1679 TYR 0.014 0.001 TYR G1591 PHE 0.008 0.001 PHE G1548 TRP 0.011 0.001 TRP G1650 HIS 0.002 0.000 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 4693) covalent geometry : angle 1.01808 / 0.42 ( 6512) hydrogen bonds : bond 0.04344 / 2.78 ( 177) hydrogen bonds : angle 4.73072 / 3.16 ( 488) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 999 MET cc_start: 0.7655 (mpp) cc_final: 0.7036 (mpp) REVERT: G 1001 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8138 (mm) REVERT: G 1240 MET cc_start: 0.6850 (mmt) cc_final: 0.6600 (mpp) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.0908 time to fit residues: 7.1959 Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1210 LEU Chi-restraints excluded: chain G residue 1665 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 45 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1097 GLN G1207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.093921 restraints weight = 7540.565| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 0.90 r_work: 0.3333 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4694 Z= 0.132 Angle : 1.010 29.599 6512 Z= 0.411 Chirality : 0.037 0.174 720 Planarity : 0.004 0.046 667 Dihedral : 24.361 110.804 947 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.51 % Allowed : 14.36 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.41), residues: 431 helix: 0.04 (0.34), residues: 228 sheet: -0.28 (0.66), residues: 67 loop : -0.79 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1679 TYR 0.012 0.001 TYR G1591 PHE 0.008 0.001 PHE G1548 TRP 0.014 0.001 TRP G1650 HIS 0.001 0.000 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 4693) covalent geometry : angle 1.00970 / 0.41 ( 6512) hydrogen bonds : bond 0.04180 / 2.70 ( 177) hydrogen bonds : angle 4.67372 / 3.11 ( 488) Misc. bond : bond 0.00004 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7649 (mpp) cc_final: 0.7022 (mpp) REVERT: G 1001 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8138 (mm) outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.0685 time to fit residues: 5.3547 Evaluate side-chains 59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1076 ASP Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1692 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093204 restraints weight = 7602.126| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 0.90 r_work: 0.3320 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4694 Z= 0.154 Angle : 1.024 29.761 6512 Z= 0.419 Chirality : 0.038 0.167 720 Planarity : 0.004 0.044 667 Dihedral : 24.315 111.181 947 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.51 % Allowed : 14.61 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.41), residues: 431 helix: 0.04 (0.34), residues: 227 sheet: -0.34 (0.66), residues: 67 loop : -0.83 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1679 TYR 0.012 0.001 TYR G1591 PHE 0.007 0.001 PHE G1079 TRP 0.010 0.001 TRP G1650 HIS 0.001 0.000 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 4693) covalent geometry : angle 1.02442 / 0.42 ( 6512) hydrogen bonds : bond 0.04452 / 2.85 ( 177) hydrogen bonds : angle 4.68099 / 3.13 ( 488) Misc. bond : bond 0.00029 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1248.94 seconds wall clock time: 22 minutes 6.75 seconds (1326.75 seconds total)