Starting phenix.real_space_refine on Tue Aug 4 16:01:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oo9_17007/08_2026/8oo9_17007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oo9_17007/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_2026/8oo9_17007.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_2026/8oo9_17007.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_2026/8oo9_17007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_2026/8oo9_17007.map" model { file = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_2026/8oo9_17007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oo9_17007/08_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-2.2rc3-6140/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: 0.74, per 1000 atoms: 0.16 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: 0.28 Conformation dependent library (CDL) restraints added in 71.4 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: 0.32 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: 0.41 Time building geometry restraints manager: 0.29 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: 2.780 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.990 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.800 ------------------------------------------------------------------------------- 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 : 1.705 70.061 6512 Z= 0.751 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 1.70530 / 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 : 0.082 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: 0.0805 time to fit residues: 10.9991 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 : 0.145 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.108002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.094166 restraints weight = 7675.463| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 0.87 r_work: 0.3337 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2405 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= 0.183 Angle : 1.122 29.425 6512 Z= 0.487 Chirality : 0.047 0.193 720 Planarity : 0.006 0.079 667 Dihedral : 24.762 149.620 947 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.01 % Allowed : 7.56 % Favored : 91.44 % 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: -1.02 (0.39), residues: 431 helix: -0.87 (0.31), residues: 220 sheet: -0.25 (0.68), residues: 65 loop : -0.19 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G1201 TYR 0.011 0.002 TYR G1018 PHE 0.016 0.002 PHE G1615 TRP 0.016 0.002 TRP G1650 HIS 0.003 0.001 HIS G1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 4693) covalent geometry : angle 1.12230 / 0.49 ( 6512) hydrogen bonds : bond 0.06988 / 4.58 ( 177) hydrogen bonds : angle 5.81873 / 3.96 ( 488) Misc. bond : bond 0.00774 / 0.41 ( 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 69 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: G 1020 ILE cc_start: 0.7483 (mm) cc_final: 0.7242 (mt) REVERT: G 1186 GLN cc_start: 0.5435 (pm20) cc_final: 0.4814 (pt0) REVERT: G 1224 TYR cc_start: 0.7800 (p90) cc_final: 0.7470 (p90) REVERT: G 1688 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6988 (tttp) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.0538 time to fit residues: 4.5617 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 : 0.083 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 0.0000 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.107418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093576 restraints weight = 7558.260| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 0.87 r_work: 0.3324 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4694 Z= 0.175 Angle : 1.060 29.441 6512 Z= 0.449 Chirality : 0.042 0.146 720 Planarity : 0.005 0.054 667 Dihedral : 24.868 146.206 947 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.76 % Allowed : 10.83 % Favored : 88.41 % 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: -0.84 (0.40), residues: 431 helix: -0.52 (0.32), residues: 227 sheet: -0.13 (0.69), residues: 65 loop : -0.49 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G1201 TYR 0.009 0.002 TYR G1230 PHE 0.012 0.002 PHE G1264 TRP 0.010 0.002 TRP G1650 HIS 0.006 0.001 HIS G1270 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 ( 4693) covalent geometry : angle 1.06021 / 0.45 ( 6512) hydrogen bonds : bond 0.05860 / 3.85 ( 177) hydrogen bonds : angle 5.35779 / 3.62 ( 488) Misc. bond : bond 0.00129 / 0.07 ( 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: 3 poor density : 60 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: G 1186 GLN cc_start: 0.5256 (pm20) cc_final: 0.4709 (pt0) REVERT: G 1224 TYR cc_start: 0.7759 (p90) cc_final: 0.7556 (p90) REVERT: G 1240 MET cc_start: 0.6243 (mmt) cc_final: 0.5826 (mpp) REVERT: G 1580 ARG cc_start: 0.7480 (mtm-85) cc_final: 0.7097 (mtm-85) REVERT: G 1688 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6943 (tttp) outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 0.0683 time to fit residues: 5.3092 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 : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.106318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.092526 restraints weight = 7538.893| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.88 r_work: 0.3303 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4694 Z= 0.185 Angle : 1.057 29.875 6512 Z= 0.444 Chirality : 0.042 0.151 720 Planarity : 0.005 0.051 667 Dihedral : 24.912 137.044 947 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.51 % Allowed : 11.84 % Favored : 86.65 % 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: -0.79 (0.40), residues: 431 helix: -0.33 (0.33), residues: 224 sheet: -0.37 (0.64), residues: 67 loop : -0.60 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G1201 TYR 0.014 0.002 TYR G1591 PHE 0.012 0.002 PHE G1079 TRP 0.009 0.002 TRP G1650 HIS 0.005 0.001 HIS G1270 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 4693) covalent geometry : angle 1.05745 / 0.44 ( 6512) hydrogen bonds : bond 0.05382 / 3.52 ( 177) hydrogen bonds : angle 5.16598 / 3.48 ( 488) Misc. bond : bond 0.00110 / 0.06 ( 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 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7712 (mpp) cc_final: 0.7132 (mpp) REVERT: G 1001 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8251 (mm) REVERT: G 1240 MET cc_start: 0.6468 (mmt) cc_final: 0.6006 (mpp) REVERT: G 1580 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.7142 (mtm180) REVERT: G 1688 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7043 (tttp) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 0.0511 time to fit residues: 4.2003 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 : 0.082 ------------------------------------------------------------------------------- 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 1100 LYS Chi-restraints excluded: chain G residue 1648 SER 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: 0.9980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.105321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.091627 restraints weight = 7577.910| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 0.87 r_work: 0.3288 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4694 Z= 0.198 Angle : 1.066 29.976 6512 Z= 0.448 Chirality : 0.041 0.135 720 Planarity : 0.004 0.046 667 Dihedral : 24.798 130.949 947 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.76 % Allowed : 12.59 % 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: -0.91 (0.40), residues: 431 helix: -0.39 (0.33), residues: 223 sheet: -0.53 (0.63), residues: 67 loop : -0.67 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G1201 TYR 0.010 0.002 TYR G 975 PHE 0.014 0.002 PHE G1079 TRP 0.010 0.002 TRP G1650 HIS 0.004 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 4693) covalent geometry : angle 1.06620 / 0.45 ( 6512) hydrogen bonds : bond 0.05389 / 3.48 ( 177) hydrogen bonds : angle 5.12407 / 3.44 ( 488) Misc. bond : bond 0.00007 / 0.00 ( 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 61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7703 (mpp) cc_final: 0.7154 (mpp) REVERT: G 1001 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8266 (mm) REVERT: G 1240 MET cc_start: 0.6607 (mmt) cc_final: 0.6115 (mpp) REVERT: G 1580 ARG cc_start: 0.7351 (mtm-85) cc_final: 0.7060 (mtm180) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.0640 time to fit residues: 4.7145 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 : 0.087 ------------------------------------------------------------------------------- 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 1648 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.105668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092094 restraints weight = 7629.540| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 0.88 r_work: 0.3300 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4694 Z= 0.179 Angle : 1.051 29.882 6512 Z= 0.437 Chirality : 0.041 0.144 720 Planarity : 0.004 0.042 667 Dihedral : 24.800 125.073 947 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.15 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: -0.80 (0.40), residues: 431 helix: -0.26 (0.34), residues: 223 sheet: -0.59 (0.63), residues: 67 loop : -0.62 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G1201 TYR 0.011 0.001 TYR G1591 PHE 0.012 0.002 PHE G1079 TRP 0.009 0.002 TRP G1650 HIS 0.003 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 4693) covalent geometry : angle 1.05130 / 0.44 ( 6512) hydrogen bonds : bond 0.05007 / 3.27 ( 177) hydrogen bonds : angle 5.06030 / 3.39 ( 488) Misc. bond : bond 0.00016 / 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 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7683 (mpp) cc_final: 0.7133 (mpp) REVERT: G 1001 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8228 (mm) REVERT: G 1240 MET cc_start: 0.6811 (mmt) cc_final: 0.6378 (mpp) REVERT: G 1580 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.7070 (mtm180) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.0765 time to fit residues: 5.9187 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 : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 977 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 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 = 0.3652 r_free = 0.3652 target = 0.106477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.092919 restraints weight = 7572.148| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 0.89 r_work: 0.3314 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3815 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= 0.152 Angle : 1.036 29.736 6512 Z= 0.427 Chirality : 0.039 0.138 720 Planarity : 0.004 0.034 667 Dihedral : 24.678 120.433 947 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.15 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: -0.77 (0.41), residues: 431 helix: -0.20 (0.34), residues: 226 sheet: -0.49 (0.65), residues: 67 loop : -0.74 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1201 TYR 0.011 0.001 TYR G 987 PHE 0.009 0.001 PHE G1548 TRP 0.009 0.002 TRP G1650 HIS 0.004 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 4693) covalent geometry : angle 1.03591 / 0.43 ( 6512) hydrogen bonds : bond 0.04702 / 3.04 ( 177) hydrogen bonds : angle 4.90836 / 3.28 ( 488) Misc. bond : bond 0.00031 / 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 62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7659 (mpp) cc_final: 0.7096 (mpp) REVERT: G 1001 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8187 (mm) REVERT: G 1240 MET cc_start: 0.6854 (mmt) cc_final: 0.6458 (mpp) REVERT: G 1580 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.7073 (mtm180) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.0828 time to fit residues: 6.3310 Evaluate side-chains 57 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.106132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.092557 restraints weight = 7649.997| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.90 r_work: 0.3306 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4694 Z= 0.159 Angle : 1.033 29.838 6512 Z= 0.426 Chirality : 0.039 0.135 720 Planarity : 0.004 0.033 667 Dihedral : 24.612 118.292 947 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.51 % Allowed : 15.11 % Favored : 83.38 % 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: -0.90 (0.40), residues: 431 helix: -0.28 (0.33), residues: 225 sheet: -0.53 (0.65), residues: 67 loop : -0.86 (0.56), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1679 TYR 0.010 0.001 TYR G1591 PHE 0.009 0.001 PHE G1079 TRP 0.009 0.001 TRP G1650 HIS 0.003 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 4693) covalent geometry : angle 1.03256 / 0.43 ( 6512) hydrogen bonds : bond 0.04735 / 3.05 ( 177) hydrogen bonds : angle 4.90114 / 3.28 ( 488) Misc. bond : bond 0.00003 / 0.00 ( 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 61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7681 (mpp) cc_final: 0.7112 (mpt) REVERT: G 1001 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8193 (mm) REVERT: G 1240 MET cc_start: 0.6854 (mmt) cc_final: 0.6467 (mpp) REVERT: G 1580 ARG cc_start: 0.7326 (mtm-85) cc_final: 0.7065 (mtm180) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 0.0803 time to fit residues: 5.8848 Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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 1648 SER 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: 0.5980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.092787 restraints weight = 7567.192| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 0.88 r_work: 0.3311 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4694 Z= 0.152 Angle : 1.034 29.759 6512 Z= 0.425 Chirality : 0.039 0.134 720 Planarity : 0.005 0.067 667 Dihedral : 24.528 115.068 947 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.27 % Allowed : 14.61 % Favored : 83.12 % 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: -0.86 (0.40), residues: 431 helix: -0.22 (0.33), residues: 225 sheet: -0.49 (0.65), residues: 67 loop : -0.91 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G1689 TYR 0.010 0.001 TYR G1591 PHE 0.008 0.001 PHE G1548 TRP 0.010 0.001 TRP G1650 HIS 0.004 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 4693) covalent geometry : angle 1.03409 / 0.43 ( 6512) hydrogen bonds : bond 0.04617 / 2.98 ( 177) hydrogen bonds : angle 4.85839 / 3.25 ( 488) Misc. bond : bond 0.00006 / 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 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: G 966 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7857 (tptp) REVERT: G 999 MET cc_start: 0.7675 (mpp) cc_final: 0.7104 (mpt) REVERT: G 1001 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8175 (mm) REVERT: G 1240 MET cc_start: 0.6906 (mmt) cc_final: 0.6602 (mpp) REVERT: G 1580 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.7038 (mtm180) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 0.0841 time to fit residues: 6.6723 Evaluate side-chains 62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 1648 SER Chi-restraints excluded: chain G residue 1665 LEU Chi-restraints excluded: chain G residue 1702 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 45 optimal weight: 7.9990 chunk 17 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G1097 GLN G1207 GLN G1692 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.107149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093664 restraints weight = 7524.612| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 0.89 r_work: 0.3326 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4133 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= 0.134 Angle : 1.030 29.665 6512 Z= 0.423 Chirality : 0.038 0.135 720 Planarity : 0.004 0.051 667 Dihedral : 24.402 110.187 947 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.02 % Allowed : 15.11 % Favored : 82.87 % 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: -0.80 (0.40), residues: 431 helix: -0.14 (0.34), residues: 227 sheet: -0.42 (0.65), residues: 67 loop : -0.97 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G1689 TYR 0.010 0.001 TYR G1224 PHE 0.008 0.001 PHE G1548 TRP 0.013 0.001 TRP G1650 HIS 0.003 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 4693) covalent geometry : angle 1.02965 / 0.42 ( 6512) hydrogen bonds : bond 0.04383 / 2.83 ( 177) hydrogen bonds : angle 4.79613 / 3.21 ( 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 62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: G 966 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7848 (tptp) REVERT: G 999 MET cc_start: 0.7671 (mpp) cc_final: 0.7017 (mpp) REVERT: G 1001 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8159 (mm) REVERT: G 1240 MET cc_start: 0.6905 (mmt) cc_final: 0.6656 (mpp) REVERT: G 1580 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.7096 (mtm180) REVERT: G 1692 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7563 (pt0) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.0754 time to fit residues: 5.6695 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 : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 968 LEU 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 1692 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 10 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 overall best weight: 0.2956 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.107162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093592 restraints weight = 7598.491| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 0.89 r_work: 0.3330 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.006 0.238 4694 Z= 0.294 Angle : 1.448 59.199 6512 Z= 0.746 Chirality : 0.045 0.659 720 Planarity : 0.004 0.053 667 Dihedral : 24.405 110.169 947 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.51 % Allowed : 15.11 % Favored : 83.38 % Cbeta Deviations : 0.24 % 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: -0.82 (0.40), residues: 431 helix: -0.16 (0.34), residues: 227 sheet: -0.42 (0.65), residues: 67 loop : -0.98 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1689 TYR 0.009 0.001 TYR G1224 PHE 0.008 0.001 PHE G1548 TRP 0.012 0.001 TRP G1650 HIS 0.003 0.001 HIS G1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.29 ( 4693) covalent geometry : angle 1.44847 / 0.75 ( 6512) hydrogen bonds : bond 0.04370 / 2.81 ( 177) hydrogen bonds : angle 4.79813 / 3.21 ( 488) Misc. bond : bond 0.00004 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 997.15 seconds wall clock time: 17 minutes 44.55 seconds (1064.55 seconds total)