Starting phenix.real_space_refine on Thu Feb 13 22:32:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tyi_20583/02_2025/6tyi_20583.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tyi_20583/02_2025/6tyi_20583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tyi_20583/02_2025/6tyi_20583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tyi_20583/02_2025/6tyi_20583.map" model { file = "/net/cci-nas-00/data/ceres_data/6tyi_20583/02_2025/6tyi_20583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tyi_20583/02_2025/6tyi_20583.cif" } resolution = 3.3 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= 0.008 sd= 0.148 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 36 5.16 5 C 5894 2.51 5 N 1567 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9184 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 4, 'TRANS': 220} Chain: "C" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1712 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "D" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1712 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "E" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1696 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain: "Y" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 236 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "Z" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.88, per 1000 atoms: 0.64 Number of scatterers: 9184 At special positions: 0 Unit cell: (84.8, 84.8, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 4 15.00 O 1683 8.00 N 1567 7.00 C 5894 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 86.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 21 through 63 removed outlier: 4.514A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 103 through 128 Processing helix chain 'A' and resid 129 through 159 removed outlier: 3.913A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 176 through 233 Proline residue: A 190 - end of helix Processing helix chain 'B' and resid 11 through 18 removed outlier: 3.597A pdb=" N HIS B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 63 Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 82 through 98 removed outlier: 4.075A pdb=" N LEU B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 127 removed outlier: 3.694A pdb=" N ILE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 162 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 170 through 233 removed outlier: 3.754A pdb=" N THR B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Proline residue: B 190 - end of helix Processing helix chain 'C' and resid 20 through 63 Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 82 through 98 Processing helix chain 'C' and resid 103 through 127 Processing helix chain 'C' and resid 129 through 163 Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 170 through 232 removed outlier: 3.567A pdb=" N ILE C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Proline residue: C 190 - end of helix Processing helix chain 'D' and resid 11 through 16 Processing helix chain 'D' and resid 21 through 63 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 82 through 98 Processing helix chain 'D' and resid 103 through 128 Processing helix chain 'D' and resid 129 through 161 removed outlier: 4.063A pdb=" N LEU D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Proline residue: D 141 - end of helix Processing helix chain 'D' and resid 170 through 233 removed outlier: 3.666A pdb=" N ALA D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.662A pdb=" N MET E 15 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR E 16 " --> pdb=" O TRP E 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 12 through 16' Processing helix chain 'E' and resid 23 through 63 removed outlier: 4.278A pdb=" N GLY E 29 " --> pdb=" O CYS E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 82 through 98 Processing helix chain 'E' and resid 103 through 127 Processing helix chain 'E' and resid 129 through 162 Proline residue: E 141 - end of helix removed outlier: 3.813A pdb=" N ALA E 160 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR E 162 " --> pdb=" O GLY E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 233 removed outlier: 3.658A pdb=" N ILE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Proline residue: E 190 - end of helix Processing helix chain 'Y' and resid 20 through 37 removed outlier: 3.962A pdb=" N VAL Y 26 " --> pdb=" O PRO Y 22 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET Y 27 " --> pdb=" O PHE Y 23 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Y 29 " --> pdb=" O ASP Y 25 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU Y 31 " --> pdb=" O MET Y 27 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE Y 34 " --> pdb=" O LEU Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 42 Processing helix chain 'Z' and resid 23 through 36 removed outlier: 3.735A pdb=" N MET Z 27 " --> pdb=" O PHE Z 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL Z 36 " --> pdb=" O ILE Z 32 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2442 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1524 1.30 - 1.43: 2284 1.43 - 1.55: 5412 1.55 - 1.68: 30 1.68 - 1.80: 67 Bond restraints: 9317 Sorted by residual: bond pdb=" C11 PGT A 301 " pdb=" O3 PGT A 301 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C31 PGT A 301 " pdb=" O2 PGT A 301 " ideal model delta sigma weight residual 1.331 1.404 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 PEV C 301 " pdb=" O2 PEV C 301 " ideal model delta sigma weight residual 1.330 1.403 -0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C31 PEV E 301 " pdb=" O2 PEV E 301 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C11 PEV C 301 " pdb=" O3 PEV C 301 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.83e+00 ... (remaining 9312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 12415 3.73 - 7.47: 140 7.47 - 11.20: 9 11.20 - 14.93: 0 14.93 - 18.66: 6 Bond angle restraints: 12570 Sorted by residual: angle pdb=" O3P PGT A 301 " pdb=" P PGT A 301 " pdb=" O4P PGT A 301 " ideal model delta sigma weight residual 92.82 111.48 -18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" O1P PEV C 301 " pdb=" P PEV C 301 " pdb=" O2P PEV C 301 " ideal model delta sigma weight residual 119.37 100.88 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" O3P PEV C 301 " pdb=" P PEV C 301 " pdb=" O4P PEV C 301 " ideal model delta sigma weight residual 93.57 111.90 -18.33 3.00e+00 1.11e-01 3.73e+01 angle pdb=" O1P PGT A 301 " pdb=" P PGT A 301 " pdb=" O2P PGT A 301 " ideal model delta sigma weight residual 119.10 100.80 18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" O3P PEV E 301 " pdb=" P PEV E 301 " pdb=" O4P PEV E 301 " ideal model delta sigma weight residual 93.57 111.77 -18.20 3.00e+00 1.11e-01 3.68e+01 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.60: 5232 25.60 - 51.19: 322 51.19 - 76.79: 49 76.79 - 102.39: 6 102.39 - 127.98: 2 Dihedral angle restraints: 5611 sinusoidal: 2239 harmonic: 3372 Sorted by residual: dihedral pdb=" CA ALA A 19 " pdb=" C ALA A 19 " pdb=" N ASP A 20 " pdb=" CA ASP A 20 " ideal model delta harmonic sigma weight residual 180.00 -157.81 -22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" C3 PEV C 301 " pdb=" C1 PEV C 301 " pdb=" C2 PEV C 301 " pdb=" O3P PEV C 301 " ideal model delta sinusoidal sigma weight residual 292.80 164.82 127.98 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C3 PEV B 301 " pdb=" C1 PEV B 301 " pdb=" C2 PEV B 301 " pdb=" O3P PEV B 301 " ideal model delta sinusoidal sigma weight residual 292.80 172.73 120.07 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 5608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 968 0.046 - 0.092: 424 0.092 - 0.138: 60 0.138 - 0.184: 10 0.184 - 0.230: 3 Chirality restraints: 1465 Sorted by residual: chirality pdb=" C5 PGT A 301 " pdb=" C4 PGT A 301 " pdb=" C6 PGT A 301 " pdb=" O5 PGT A 301 " both_signs ideal model delta sigma weight residual False -2.30 -2.53 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C2 PGT A 301 " pdb=" C1 PGT A 301 " pdb=" C3 PGT A 301 " pdb=" O2 PGT A 301 " both_signs ideal model delta sigma weight residual False 2.35 2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL B 197 " pdb=" CA VAL B 197 " pdb=" CG1 VAL B 197 " pdb=" CG2 VAL B 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1462 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 113 " 0.017 2.00e-02 2.50e+03 1.73e-02 5.26e+00 pdb=" CG PHE A 113 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 113 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 113 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 113 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 113 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 113 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 140 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 141 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 171 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO E 172 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 172 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 172 " -0.022 5.00e-02 4.00e+02 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 21 2.42 - 3.04: 6027 3.04 - 3.66: 13193 3.66 - 4.28: 19345 4.28 - 4.90: 32973 Nonbonded interactions: 71559 Sorted by model distance: nonbonded pdb=" OG SER D 98 " pdb=" NH1 ARG D 110 " model vdw 1.796 3.120 nonbonded pdb=" OG SER A 98 " pdb=" NH1 ARG A 110 " model vdw 2.179 3.120 nonbonded pdb=" OE2 GLU A 58 " pdb=" OG SER A 82 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR A 148 " pdb=" O ALA A 177 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU B 58 " pdb=" OG SER B 82 " model vdw 2.241 3.040 ... (remaining 71554 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 233) selection = (chain 'B' and resid 11 through 233) selection = (chain 'C' and resid 11 through 233) selection = (chain 'D' and resid 11 through 233) selection = (chain 'E' and resid 11 through 233) } ncs_group { reference = (chain 'Y' and resid 12 through 40) selection = chain 'Z' } 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=1.00 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.300 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.012 0.104 9317 Z= 0.732 Angle : 1.033 18.665 12570 Z= 0.504 Chirality : 0.049 0.230 1465 Planarity : 0.004 0.039 1598 Dihedral : 16.668 127.984 3433 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 0.43 % Allowed : 10.99 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.22), residues: 1172 helix: 0.18 (0.15), residues: 996 sheet: None (None), residues: 0 loop : -4.46 (0.30), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 38 HIS 0.009 0.001 HIS Z 16 PHE 0.040 0.003 PHE A 113 TYR 0.016 0.002 TYR D 132 ARG 0.009 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.953 Fit side-chains REVERT: A 94 GLU cc_start: 0.8723 (tp30) cc_final: 0.8202 (tp30) REVERT: B 126 MET cc_start: 0.8051 (mmm) cc_final: 0.7533 (mmt) REVERT: C 64 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 94 GLU cc_start: 0.5571 (mm-30) cc_final: 0.5213 (mm-30) REVERT: D 128 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7521 (ttp-110) REVERT: E 226 LEU cc_start: 0.8851 (mt) cc_final: 0.8548 (mp) outliers start: 4 outliers final: 3 residues processed: 152 average time/residue: 0.2885 time to fit residues: 56.6949 Evaluate side-chains 126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 186 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN B 70 GLN B 93 ASN C 215 GLN D 93 ASN D 125 GLN D 196 ASN E 69 ASN E 93 ASN E 196 ASN Z 16 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.169712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134243 restraints weight = 10130.604| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.95 r_work: 0.3383 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9317 Z= 0.185 Angle : 0.519 6.805 12570 Z= 0.266 Chirality : 0.035 0.127 1465 Planarity : 0.003 0.030 1598 Dihedral : 12.078 126.591 1440 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.83 % Allowed : 15.73 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.24), residues: 1172 helix: 2.05 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -4.17 (0.35), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 38 HIS 0.003 0.000 HIS Z 16 PHE 0.019 0.001 PHE A 113 TYR 0.009 0.001 TYR A 132 ARG 0.006 0.000 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: B 94 GLU cc_start: 0.8903 (tp30) cc_final: 0.8698 (tp30) REVERT: B 96 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 126 MET cc_start: 0.7660 (mmm) cc_final: 0.7400 (mmt) REVERT: B 153 MET cc_start: 0.8555 (ttp) cc_final: 0.8228 (ttt) REVERT: C 93 ASN cc_start: 0.8411 (t0) cc_final: 0.7931 (t0) REVERT: C 118 ARG cc_start: 0.7230 (tpm170) cc_final: 0.6860 (mmm-85) REVERT: D 200 ARG cc_start: 0.8092 (mmm160) cc_final: 0.6869 (mtp180) REVERT: E 226 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8148 (mp) REVERT: Z 15 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7860 (mtt) outliers start: 17 outliers final: 7 residues processed: 125 average time/residue: 0.2862 time to fit residues: 46.4629 Evaluate side-chains 119 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Z residue 15 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 64 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.171270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135857 restraints weight = 10307.063| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.96 r_work: 0.3401 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9317 Z= 0.174 Angle : 0.492 6.813 12570 Z= 0.249 Chirality : 0.035 0.127 1465 Planarity : 0.003 0.053 1598 Dihedral : 11.734 127.580 1439 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.83 % Allowed : 17.03 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.96 (0.25), residues: 1172 helix: 2.74 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -3.86 (0.37), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 38 HIS 0.001 0.000 HIS Z 16 PHE 0.014 0.001 PHE A 113 TYR 0.008 0.001 TYR D 132 ARG 0.004 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.933 Fit side-chains REVERT: A 64 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8262 (pt0) REVERT: B 94 GLU cc_start: 0.8908 (tp30) cc_final: 0.8620 (tp30) REVERT: B 96 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 126 MET cc_start: 0.7595 (mmm) cc_final: 0.7317 (mmt) REVERT: B 153 MET cc_start: 0.8577 (ttp) cc_final: 0.8206 (ttt) REVERT: C 118 ARG cc_start: 0.7360 (tpm170) cc_final: 0.6917 (mmm-85) REVERT: D 200 ARG cc_start: 0.8080 (mmm160) cc_final: 0.6913 (mtp180) REVERT: E 99 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7843 (pt0) REVERT: E 226 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8117 (mp) REVERT: Z 15 MET cc_start: 0.8143 (mtm) cc_final: 0.7885 (mtt) outliers start: 17 outliers final: 9 residues processed: 116 average time/residue: 0.2718 time to fit residues: 41.7218 Evaluate side-chains 114 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 226 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.189568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155090 restraints weight = 9854.535| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.86 r_work: 0.3674 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9317 Z= 0.149 Angle : 0.463 6.822 12570 Z= 0.235 Chirality : 0.034 0.118 1465 Planarity : 0.003 0.043 1598 Dihedral : 11.096 124.166 1438 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.69 % Allowed : 17.35 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.54 (0.25), residues: 1172 helix: 3.12 (0.16), residues: 1016 sheet: None (None), residues: 0 loop : -3.64 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.001 0.000 HIS Z 16 PHE 0.011 0.001 PHE A 113 TYR 0.007 0.001 TYR B 132 ARG 0.004 0.000 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8100 (pt0) REVERT: A 94 GLU cc_start: 0.8595 (tp30) cc_final: 0.8108 (tp30) REVERT: A 223 ASP cc_start: 0.7811 (m-30) cc_final: 0.7509 (m-30) REVERT: B 96 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7830 (mt-10) REVERT: B 153 MET cc_start: 0.8453 (ttp) cc_final: 0.8070 (ttt) REVERT: D 153 MET cc_start: 0.6890 (ttp) cc_final: 0.6605 (ttt) REVERT: D 200 ARG cc_start: 0.7874 (mmm160) cc_final: 0.6961 (mtp180) REVERT: E 93 ASN cc_start: 0.8774 (t0) cc_final: 0.8556 (t0) REVERT: E 99 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: E 215 GLN cc_start: 0.8157 (tp40) cc_final: 0.7547 (tt0) REVERT: E 226 LEU cc_start: 0.8517 (mt) cc_final: 0.8222 (mp) REVERT: Z 35 MET cc_start: 0.7807 (tpp) cc_final: 0.7547 (mmt) outliers start: 25 outliers final: 16 residues processed: 130 average time/residue: 0.2451 time to fit residues: 42.9913 Evaluate side-chains 120 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 82 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.189483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154600 restraints weight = 9955.954| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.87 r_work: 0.3665 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9317 Z= 0.165 Angle : 0.469 6.764 12570 Z= 0.236 Chirality : 0.034 0.118 1465 Planarity : 0.003 0.065 1598 Dihedral : 10.830 122.038 1438 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.80 % Allowed : 18.21 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.75 (0.25), residues: 1172 helix: 3.25 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : -3.46 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.001 0.000 HIS Z 16 PHE 0.010 0.001 PHE Z 23 TYR 0.009 0.001 TYR B 16 ARG 0.004 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8059 (pt0) REVERT: A 223 ASP cc_start: 0.7747 (m-30) cc_final: 0.7361 (m-30) REVERT: B 96 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 153 MET cc_start: 0.8455 (ttp) cc_final: 0.8054 (ttt) REVERT: D 128 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7171 (ttp-170) REVERT: D 153 MET cc_start: 0.6891 (ttp) cc_final: 0.6605 (ttt) REVERT: D 200 ARG cc_start: 0.7605 (mmm160) cc_final: 0.6768 (mtm110) REVERT: E 226 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8228 (mp) outliers start: 26 outliers final: 18 residues processed: 124 average time/residue: 0.2568 time to fit residues: 43.0533 Evaluate side-chains 119 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.186934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151880 restraints weight = 9883.006| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.87 r_work: 0.3636 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9317 Z= 0.211 Angle : 0.495 7.745 12570 Z= 0.247 Chirality : 0.035 0.178 1465 Planarity : 0.003 0.051 1598 Dihedral : 10.572 121.037 1438 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.80 % Allowed : 18.43 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.73 (0.25), residues: 1172 helix: 3.22 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : -3.36 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.002 0.000 HIS Z 16 PHE 0.012 0.001 PHE A 113 TYR 0.007 0.001 TYR D 132 ARG 0.003 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8083 (pt0) REVERT: A 223 ASP cc_start: 0.7745 (m-30) cc_final: 0.7329 (m-30) REVERT: B 96 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7831 (mt-10) REVERT: B 153 MET cc_start: 0.8463 (ttp) cc_final: 0.8064 (ttt) REVERT: C 114 ARG cc_start: 0.6387 (tpm170) cc_final: 0.6066 (tpm170) REVERT: D 128 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7324 (ttp-170) REVERT: D 153 MET cc_start: 0.6924 (ttp) cc_final: 0.6656 (ttt) REVERT: D 200 ARG cc_start: 0.7516 (mmm160) cc_final: 0.6678 (mtm110) REVERT: E 99 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: E 226 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8198 (mp) outliers start: 26 outliers final: 18 residues processed: 123 average time/residue: 0.2480 time to fit residues: 40.9666 Evaluate side-chains 125 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 104 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN E 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.163349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124405 restraints weight = 9444.165| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.94 r_work: 0.3235 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9317 Z= 0.187 Angle : 0.484 7.946 12570 Z= 0.243 Chirality : 0.035 0.152 1465 Planarity : 0.004 0.094 1598 Dihedral : 10.330 118.866 1438 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.69 % Allowed : 19.07 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.84 (0.25), residues: 1172 helix: 3.29 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : -3.31 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.003 0.000 HIS A 86 PHE 0.010 0.001 PHE Z 23 TYR 0.007 0.001 TYR D 132 ARG 0.004 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7894 (pt0) REVERT: A 181 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7270 (m) REVERT: A 223 ASP cc_start: 0.7513 (m-30) cc_final: 0.6970 (m-30) REVERT: B 96 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7632 (mt-10) REVERT: B 153 MET cc_start: 0.8178 (ttp) cc_final: 0.7802 (ttt) REVERT: C 64 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 114 ARG cc_start: 0.6145 (tpm170) cc_final: 0.5839 (tpm170) REVERT: D 128 ARG cc_start: 0.7619 (ttm170) cc_final: 0.6847 (ttp-170) REVERT: D 153 MET cc_start: 0.6514 (ttp) cc_final: 0.6256 (ttt) REVERT: D 200 ARG cc_start: 0.7366 (mmm160) cc_final: 0.6186 (mtm110) REVERT: E 99 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: E 226 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7797 (mp) REVERT: Z 35 MET cc_start: 0.7747 (tpp) cc_final: 0.7294 (mmt) outliers start: 25 outliers final: 16 residues processed: 124 average time/residue: 0.2548 time to fit residues: 42.3983 Evaluate side-chains 118 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Z 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.164557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125520 restraints weight = 9570.993| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.96 r_work: 0.3241 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9317 Z= 0.163 Angle : 0.472 8.314 12570 Z= 0.238 Chirality : 0.034 0.137 1465 Planarity : 0.003 0.067 1598 Dihedral : 10.064 114.598 1437 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.69 % Allowed : 19.29 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.96 (0.25), residues: 1172 helix: 3.37 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : -3.23 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.002 0.000 HIS Z 16 PHE 0.010 0.001 PHE Z 23 TYR 0.012 0.001 TYR C 16 ARG 0.006 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7936 (pt0) REVERT: A 223 ASP cc_start: 0.7512 (m-30) cc_final: 0.6938 (m-30) REVERT: B 96 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7764 (mt-10) REVERT: B 153 MET cc_start: 0.8064 (ttp) cc_final: 0.7724 (ttt) REVERT: C 64 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 118 ARG cc_start: 0.7116 (tpm170) cc_final: 0.6581 (mmm-85) REVERT: D 128 ARG cc_start: 0.7385 (ttm170) cc_final: 0.6473 (ttp-170) REVERT: D 153 MET cc_start: 0.6375 (ttp) cc_final: 0.6130 (ttt) REVERT: D 200 ARG cc_start: 0.7330 (mmm160) cc_final: 0.6081 (mtm110) REVERT: E 99 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7469 (pt0) REVERT: E 208 MET cc_start: 0.7926 (ttp) cc_final: 0.7724 (ttm) REVERT: E 226 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7568 (mp) REVERT: Z 35 MET cc_start: 0.7805 (tpp) cc_final: 0.7342 (mmt) outliers start: 25 outliers final: 17 residues processed: 126 average time/residue: 0.2554 time to fit residues: 42.7368 Evaluate side-chains 121 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 110 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN C 201 GLN Z 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.161315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122224 restraints weight = 9407.848| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.93 r_work: 0.3200 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9317 Z= 0.236 Angle : 0.509 8.355 12570 Z= 0.254 Chirality : 0.036 0.130 1465 Planarity : 0.003 0.061 1598 Dihedral : 9.993 109.166 1437 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.69 % Allowed : 19.29 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.80 (0.25), residues: 1172 helix: 3.26 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : -3.21 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.002 0.000 HIS Z 16 PHE 0.009 0.001 PHE Z 23 TYR 0.013 0.001 TYR C 16 ARG 0.006 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7954 (pt0) REVERT: A 181 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7469 (m) REVERT: A 223 ASP cc_start: 0.7554 (m-30) cc_final: 0.6962 (m-30) REVERT: B 96 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7759 (mt-10) REVERT: B 153 MET cc_start: 0.8087 (ttp) cc_final: 0.7735 (ttt) REVERT: C 64 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8198 (tm-30) REVERT: C 114 ARG cc_start: 0.6463 (tpm170) cc_final: 0.6157 (tpm170) REVERT: D 153 MET cc_start: 0.6470 (ttp) cc_final: 0.6235 (ttt) REVERT: D 200 ARG cc_start: 0.7286 (mmm160) cc_final: 0.6094 (mtm110) REVERT: E 99 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: E 208 MET cc_start: 0.8050 (ttp) cc_final: 0.7847 (ttm) REVERT: Z 35 MET cc_start: 0.7797 (tpp) cc_final: 0.7334 (mmt) outliers start: 25 outliers final: 19 residues processed: 130 average time/residue: 0.2397 time to fit residues: 42.3403 Evaluate side-chains 129 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Z 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.160618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121533 restraints weight = 9561.942| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.93 r_work: 0.3191 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9317 Z= 0.241 Angle : 0.515 8.179 12570 Z= 0.258 Chirality : 0.036 0.125 1465 Planarity : 0.003 0.060 1598 Dihedral : 10.013 104.005 1437 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.26 % Allowed : 20.15 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.74 (0.25), residues: 1172 helix: 3.22 (0.15), residues: 1014 sheet: None (None), residues: 0 loop : -3.19 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.002 0.000 HIS Z 16 PHE 0.010 0.001 PHE Z 23 TYR 0.016 0.001 TYR C 16 ARG 0.004 0.000 ARG A 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7934 (pt0) REVERT: A 181 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7478 (m) REVERT: A 223 ASP cc_start: 0.7575 (m-30) cc_final: 0.6988 (m-30) REVERT: B 96 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7760 (mt-10) REVERT: B 153 MET cc_start: 0.8107 (ttp) cc_final: 0.7755 (ttt) REVERT: C 64 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8196 (tm-30) REVERT: C 114 ARG cc_start: 0.6477 (tpm170) cc_final: 0.6169 (tpm170) REVERT: D 153 MET cc_start: 0.6413 (ttp) cc_final: 0.6185 (ttt) REVERT: D 200 ARG cc_start: 0.7293 (mmm160) cc_final: 0.6095 (mtm110) REVERT: E 99 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: E 208 MET cc_start: 0.8048 (ttp) cc_final: 0.7848 (ttm) REVERT: Z 35 MET cc_start: 0.7812 (tpp) cc_final: 0.7349 (mmt) outliers start: 21 outliers final: 17 residues processed: 128 average time/residue: 0.2451 time to fit residues: 42.4057 Evaluate side-chains 126 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 200 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Z 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.157194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117752 restraints weight = 9543.837| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.92 r_work: 0.3134 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9317 Z= 0.374 Angle : 0.599 8.025 12570 Z= 0.300 Chirality : 0.039 0.133 1465 Planarity : 0.003 0.060 1598 Dihedral : 10.354 101.302 1437 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.48 % Allowed : 20.15 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.29 (0.25), residues: 1172 helix: 2.90 (0.15), residues: 1014 sheet: None (None), residues: 0 loop : -3.21 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.003 0.000 HIS Z 16 PHE 0.011 0.001 PHE A 113 TYR 0.016 0.001 TYR C 16 ARG 0.004 0.001 ARG A 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3880.26 seconds wall clock time: 69 minutes 31.57 seconds (4171.57 seconds total)