Starting phenix.real_space_refine on Tue Feb 11 07:42:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oo9_17007/02_2025/8oo9_17007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oo9_17007/02_2025/8oo9_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_17007/02_2025/8oo9_17007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oo9_17007/02_2025/8oo9_17007.map" model { file = "/net/cci-nas-00/data/ceres_data/8oo9_17007/02_2025/8oo9_17007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oo9_17007/02_2025/8oo9_17007.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.87, per 1000 atoms: 0.86 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: 1.33 Conformation dependent library (CDL) restraints added in 445.0 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: 1.77 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: 1.85 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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=" 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=" F4 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.686 1.778 -0.092 2.00e-02 2.50e+03 2.09e+01 bond pdb=" F2 ALF G2003 " pdb="AL ALF G2003 " ideal model delta sigma weight residual 1.685 1.775 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C4' DG L -36 " pdb=" C3' DG L -36 " ideal model delta sigma weight residual 1.523 1.587 -0.064 2.00e-02 2.50e+03 1.04e+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: 442 0.054 - 0.107: 219 0.107 - 0.160: 49 0.160 - 0.214: 8 0.214 - 0.267: 2 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=" 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 chirality pdb=" CB ILE G1701 " pdb=" CA ILE G1701 " pdb=" CG1 ILE G1701 " pdb=" CG2 ILE G1701 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.10e+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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.010 0.115 4693 Z= 0.603 Angle : 1.701 70.061 6512 Z= 0.727 Chirality : 0.064 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 : 4.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (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 TRP 0.042 0.004 TRP G1650 HIS 0.011 0.002 HIS G1663 PHE 0.039 0.005 PHE G1079 TYR 0.025 0.006 TYR G1588 ARG 0.036 0.004 ARG G1201 *********************** 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 : 0.466 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: 0.2855 time to fit residues: 38.4905 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 : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1663 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.093935 restraints weight = 7532.282| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 0.87 r_work: 0.3328 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4693 Z= 0.250 Angle : 1.060 29.438 6512 Z= 0.447 Chirality : 0.040 0.144 720 Planarity : 0.005 0.063 667 Dihedral : 24.586 144.958 947 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.76 % Allowed : 7.56 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.39), residues: 431 helix: -0.67 (0.31), residues: 227 sheet: -0.20 (0.69), residues: 65 loop : -0.37 (0.56), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G1650 HIS 0.003 0.001 HIS G1663 PHE 0.015 0.002 PHE G1615 TYR 0.010 0.001 TYR G 975 ARG 0.007 0.001 ARG G1201 *********************** 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 76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: G 999 MET cc_start: 0.7649 (mpp) cc_final: 0.7161 (mpp) REVERT: G 1047 PHE cc_start: 0.8726 (m-10) cc_final: 0.8451 (m-80) REVERT: G 1186 GLN cc_start: 0.5429 (pm20) cc_final: 0.4858 (pt0) REVERT: G 1224 TYR cc_start: 0.7887 (p90) cc_final: 0.7626 (p90) REVERT: G 1688 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6962 (tttp) outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.2225 time to fit residues: 20.3215 Evaluate side-chains 62 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1076 ASP 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 9 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 0.0270 chunk 22 optimal weight: 0.0050 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1035 ASN G1144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095862 restraints weight = 7476.231| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.87 r_work: 0.3369 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4693 Z= 0.170 Angle : 1.008 29.677 6512 Z= 0.410 Chirality : 0.036 0.124 720 Planarity : 0.003 0.035 667 Dihedral : 24.139 127.407 947 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.76 % Allowed : 12.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.40), residues: 431 helix: -0.02 (0.33), residues: 228 sheet: -0.05 (0.69), residues: 67 loop : -0.37 (0.55), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G1053 HIS 0.008 0.001 HIS G1191 PHE 0.009 0.001 PHE G1548 TYR 0.008 0.001 TYR G 975 ARG 0.006 0.001 ARG G1679 *********************** 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 70 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: G 1186 GLN cc_start: 0.5149 (pm20) cc_final: 0.4898 (tt0) REVERT: G 1224 TYR cc_start: 0.8017 (p90) cc_final: 0.7813 (p90) outliers start: 3 outliers final: 1 residues processed: 68 average time/residue: 0.2270 time to fit residues: 18.6727 Evaluate side-chains 61 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1076 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN ** G1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092442 restraints weight = 7432.569| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 0.88 r_work: 0.3299 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4693 Z= 0.263 Angle : 1.038 30.385 6512 Z= 0.429 Chirality : 0.038 0.125 720 Planarity : 0.004 0.051 667 Dihedral : 24.204 115.141 947 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.26 % Allowed : 13.35 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.40), residues: 431 helix: -0.06 (0.33), residues: 228 sheet: -0.13 (0.68), residues: 67 loop : -0.54 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G1650 HIS 0.003 0.001 HIS G1191 PHE 0.011 0.002 PHE G1079 TYR 0.012 0.001 TYR G 975 ARG 0.005 0.001 ARG G1201 *********************** 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 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 0.1922 time to fit residues: 14.9921 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 25 optimal weight: 0.0030 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN ** G1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.106547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092980 restraints weight = 7596.032| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.89 r_work: 0.3313 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4693 Z= 0.213 Angle : 1.009 29.749 6512 Z= 0.410 Chirality : 0.036 0.121 720 Planarity : 0.004 0.033 667 Dihedral : 23.791 106.135 947 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.76 % Allowed : 13.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.40), residues: 431 helix: 0.03 (0.33), residues: 228 sheet: -0.26 (0.66), residues: 67 loop : -0.64 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1650 HIS 0.002 0.001 HIS G1191 PHE 0.009 0.001 PHE G1548 TYR 0.010 0.001 TYR G1224 ARG 0.004 0.000 ARG G1201 *********************** 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 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: G 1157 LEU cc_start: 0.7540 (mp) cc_final: 0.7284 (mt) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.2172 time to fit residues: 16.7163 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 : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN G1140 GLN ** G1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090482 restraints weight = 7531.559| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 0.88 r_work: 0.3261 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4693 Z= 0.339 Angle : 1.060 31.071 6512 Z= 0.441 Chirality : 0.040 0.136 720 Planarity : 0.005 0.054 667 Dihedral : 24.076 110.179 947 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.52 % Allowed : 12.34 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.39), residues: 431 helix: -0.23 (0.33), residues: 227 sheet: -0.58 (0.64), residues: 67 loop : -0.81 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G1650 HIS 0.002 0.001 HIS G1080 PHE 0.015 0.002 PHE G1079 TYR 0.021 0.002 TYR G1591 ARG 0.005 0.001 ARG G1201 *********************** 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 66 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: G 1131 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6822 (mtt90) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.2763 time to fit residues: 20.8280 Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE 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 1131 ARG Chi-restraints excluded: chain G residue 1210 LEU Chi-restraints excluded: chain G residue 1648 SER Chi-restraints excluded: chain G residue 1691 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 41 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3628 r_free = 0.3628 target = 0.105242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092204 restraints weight = 7517.300| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 0.87 r_work: 0.3299 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4693 Z= 0.222 Angle : 1.017 30.096 6512 Z= 0.413 Chirality : 0.037 0.124 720 Planarity : 0.004 0.035 667 Dihedral : 23.754 107.224 947 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.27 % Allowed : 12.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.40), residues: 431 helix: -0.01 (0.34), residues: 227 sheet: -0.52 (0.64), residues: 67 loop : -0.91 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G1650 HIS 0.002 0.000 HIS G1663 PHE 0.008 0.001 PHE G1548 TYR 0.013 0.001 TYR G1591 ARG 0.011 0.001 ARG G1689 *********************** 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 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.536 Fit side-chains REVERT: G 966 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7806 (tptp) REVERT: G 1001 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8162 (mm) REVERT: G 1131 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6962 (mtp85) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.2484 time to fit residues: 18.7810 Evaluate side-chains 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE Chi-restraints excluded: chain G residue 1001 LEU Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1100 LYS Chi-restraints excluded: chain G residue 1131 ARG Chi-restraints excluded: chain G residue 1210 LEU Chi-restraints excluded: chain G residue 1648 SER Chi-restraints excluded: chain G residue 1691 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN G1151 HIS ** G1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.090683 restraints weight = 7586.470| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 0.87 r_work: 0.3267 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4693 Z= 0.320 Angle : 1.056 30.508 6512 Z= 0.437 Chirality : 0.040 0.146 720 Planarity : 0.005 0.046 667 Dihedral : 23.826 108.132 947 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.52 % Allowed : 14.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.39), residues: 431 helix: -0.24 (0.33), residues: 227 sheet: -0.67 (0.65), residues: 67 loop : -1.03 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G1036 HIS 0.002 0.001 HIS G1080 PHE 0.012 0.002 PHE G1079 TYR 0.015 0.002 TYR G1018 ARG 0.007 0.001 ARG G1679 *********************** 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: 10 poor density : 51 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: G 966 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7853 (tptp) REVERT: G 1001 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8276 (mm) REVERT: G 1131 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6882 (mtt90) REVERT: G 1240 MET cc_start: 0.7381 (mpp) cc_final: 0.7149 (mpp) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.2294 time to fit residues: 16.3302 Evaluate side-chains 58 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE 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 1131 ARG Chi-restraints excluded: chain G residue 1210 LEU Chi-restraints excluded: chain G residue 1648 SER Chi-restraints excluded: chain G residue 1691 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 40 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3627 r_free = 0.3627 target = 0.105466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092564 restraints weight = 7570.133| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 0.88 r_work: 0.3302 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4693 Z= 0.229 Angle : 1.021 30.563 6512 Z= 0.416 Chirality : 0.037 0.161 720 Planarity : 0.004 0.034 667 Dihedral : 23.632 106.040 947 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.52 % Allowed : 15.11 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.40), residues: 431 helix: -0.09 (0.33), residues: 228 sheet: -0.46 (0.66), residues: 67 loop : -1.01 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G1036 HIS 0.002 0.000 HIS G1191 PHE 0.008 0.001 PHE G1548 TYR 0.009 0.001 TYR G1591 ARG 0.006 0.000 ARG G1679 *********************** 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: 10 poor density : 54 time to evaluate : 0.500 Fit side-chains REVERT: G 966 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7835 (tptp) REVERT: G 1001 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8225 (mm) REVERT: G 1131 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.6910 (mtp85) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.2447 time to fit residues: 18.3110 Evaluate side-chains 59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE 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 1131 ARG Chi-restraints excluded: chain G residue 1210 LEU Chi-restraints excluded: chain G residue 1648 SER Chi-restraints excluded: chain G residue 1691 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 10 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1097 GLN ** G1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091793 restraints weight = 7603.196| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 0.87 r_work: 0.3287 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4693 Z= 0.263 Angle : 1.036 30.683 6512 Z= 0.423 Chirality : 0.039 0.145 720 Planarity : 0.004 0.038 667 Dihedral : 23.603 105.801 947 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.27 % Allowed : 15.62 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.40), residues: 431 helix: -0.14 (0.33), residues: 227 sheet: -0.54 (0.66), residues: 67 loop : -1.08 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G1036 HIS 0.002 0.000 HIS G1191 PHE 0.010 0.001 PHE G1079 TYR 0.017 0.002 TYR G1018 ARG 0.007 0.001 ARG G1689 ********************** 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 60 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.403 Fit side-chains REVERT: G 966 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7846 (tptp) REVERT: G 1001 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8237 (mm) REVERT: G 1131 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.6962 (mtp85) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.2242 time to fit residues: 15.8511 Evaluate side-chains 59 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 991 ILE 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 1131 ARG Chi-restraints excluded: chain G residue 1648 SER Chi-restraints excluded: chain G residue 1691 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.0470 chunk 29 optimal weight: 0.3980 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3632 r_free = 0.3632 target = 0.105813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093039 restraints weight = 7449.019| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 0.87 r_work: 0.3309 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4693 Z= 0.212 Angle : 1.016 30.598 6512 Z= 0.412 Chirality : 0.037 0.131 720 Planarity : 0.004 0.036 667 Dihedral : 23.418 101.863 947 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.76 % Allowed : 15.87 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.40), residues: 431 helix: 0.00 (0.34), residues: 228 sheet: -0.46 (0.67), residues: 67 loop : -1.04 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1650 HIS 0.001 0.000 HIS G1191 PHE 0.008 0.001 PHE G1548 TYR 0.009 0.001 TYR G1591 ARG 0.006 0.000 ARG G1689 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.23 seconds wall clock time: 45 minutes 22.19 seconds (2722.19 seconds total)