Starting phenix.real_space_refine on Tue Feb 3 12:51:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ck6_45642/02_2026/9ck6_45642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ck6_45642/02_2026/9ck6_45642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ck6_45642/02_2026/9ck6_45642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ck6_45642/02_2026/9ck6_45642.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ck6_45642/02_2026/9ck6_45642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ck6_45642/02_2026/9ck6_45642.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1630 2.51 5 N 420 2.21 5 O 450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2510 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Restraints were copied for chains: A, B, C, D, E, F, G, H, I Time building chain proxies: 0.28, per 1000 atoms: 0.11 Number of scatterers: 2510 At special positions: 0 Unit cell: (63.012, 71.556, 48.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 450 8.00 N 420 7.00 C 1630 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=0, symmetry=0 Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 95.6 milliseconds 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.794A pdb=" N TYR R 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N HIS D 13 " --> pdb=" O TYR R 10 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL R 12 " --> pdb=" O HIS D 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.281A pdb=" N LEU R 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE D 20 " --> pdb=" O LEU R 17 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE R 19 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE R 20 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE B 20 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE F 20 " --> pdb=" O PHE H 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 30 through 36 removed outlier: 9.173A pdb=" N ALA R 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N GLY D 33 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE R 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET D 35 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU R 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU R 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET B 35 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL R 36 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET F 35 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 36 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE F 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE H 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY F 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.419A pdb=" N VAL R 40 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL B 40 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 40 " --> pdb=" O ILE H 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.899A pdb=" N TYR A 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N HIS E 13 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 16 through 20 removed outlier: 6.333A pdb=" N LEU A 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE E 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE A 19 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE A 20 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE C 20 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE G 20 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 30 through 36 removed outlier: 6.199A pdb=" N ILE A 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU E 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY A 33 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N VAL E 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N MET A 35 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET C 35 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 36 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU C 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET G 35 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 36 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU G 34 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET I 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL G 36 " --> pdb=" O MET I 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.466A pdb=" N VAL A 40 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL C 40 " --> pdb=" O ILE G 41 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL G 40 " --> pdb=" O ILE I 41 " (cutoff:3.500A) 58 hydrogen bonds defined for protein. 174 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: 0.32 Time building geometry restraints manager: 0.23 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: 820 1.34 - 1.45: 305 1.45 - 1.56: 1405 1.56 - 1.68: 0 1.68 - 1.79: 20 Bond restraints: 2550 Sorted by residual: bond pdb=" CG1 ILE I 31 " pdb=" CD1 ILE I 31 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.71e-01 bond pdb=" CG1 ILE H 31 " pdb=" CD1 ILE H 31 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.69e-01 bond pdb=" CG1 ILE F 31 " pdb=" CD1 ILE F 31 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.58e-01 bond pdb=" CG1 ILE B 31 " pdb=" CD1 ILE B 31 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.55e-01 bond pdb=" CG1 ILE D 31 " pdb=" CD1 ILE D 31 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.50e-01 ... (remaining 2545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.74: 2994 0.74 - 1.48: 325 1.48 - 2.21: 71 2.21 - 2.95: 30 2.95 - 3.69: 10 Bond angle restraints: 3430 Sorted by residual: angle pdb=" N GLU R 22 " pdb=" CA GLU R 22 " pdb=" C GLU R 22 " ideal model delta sigma weight residual 108.34 112.03 -3.69 1.31e+00 5.83e-01 7.93e+00 angle pdb=" N GLU D 22 " pdb=" CA GLU D 22 " pdb=" C GLU D 22 " ideal model delta sigma weight residual 108.34 112.03 -3.69 1.31e+00 5.83e-01 7.92e+00 angle pdb=" N GLU I 22 " pdb=" CA GLU I 22 " pdb=" C GLU I 22 " ideal model delta sigma weight residual 108.34 112.02 -3.68 1.31e+00 5.83e-01 7.88e+00 angle pdb=" N GLU G 22 " pdb=" CA GLU G 22 " pdb=" C GLU G 22 " ideal model delta sigma weight residual 108.34 112.01 -3.67 1.31e+00 5.83e-01 7.87e+00 angle pdb=" N GLU E 22 " pdb=" CA GLU E 22 " pdb=" C GLU E 22 " ideal model delta sigma weight residual 108.34 112.01 -3.67 1.31e+00 5.83e-01 7.86e+00 ... (remaining 3425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.81: 1120 9.81 - 19.62: 160 19.62 - 29.43: 80 29.43 - 39.23: 40 39.23 - 49.04: 20 Dihedral angle restraints: 1420 sinusoidal: 520 harmonic: 900 Sorted by residual: dihedral pdb=" CA LEU R 17 " pdb=" CB LEU R 17 " pdb=" CG LEU R 17 " pdb=" CD1 LEU R 17 " ideal model delta sinusoidal sigma weight residual 180.00 139.66 40.34 3 1.50e+01 4.44e-03 7.18e+00 dihedral pdb=" CA LEU F 17 " pdb=" CB LEU F 17 " pdb=" CG LEU F 17 " pdb=" CD1 LEU F 17 " ideal model delta sinusoidal sigma weight residual 180.00 139.68 40.32 3 1.50e+01 4.44e-03 7.18e+00 dihedral pdb=" CA LEU G 17 " pdb=" CB LEU G 17 " pdb=" CG LEU G 17 " pdb=" CD1 LEU G 17 " ideal model delta sinusoidal sigma weight residual 180.00 139.68 40.32 3 1.50e+01 4.44e-03 7.18e+00 ... (remaining 1417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 137 0.029 - 0.059: 133 0.059 - 0.088: 32 0.088 - 0.117: 52 0.117 - 0.147: 36 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE G 31 " pdb=" N ILE G 31 " pdb=" C ILE G 31 " pdb=" CB ILE G 31 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE B 31 " pdb=" N ILE B 31 " pdb=" C ILE B 31 " pdb=" CB ILE B 31 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 387 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 11 " 0.002 2.00e-02 2.50e+03 4.22e-03 1.78e-01 pdb=" C GLU B 11 " -0.007 2.00e-02 2.50e+03 pdb=" O GLU B 11 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL B 12 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 11 " -0.002 2.00e-02 2.50e+03 3.99e-03 1.59e-01 pdb=" C GLU A 11 " 0.007 2.00e-02 2.50e+03 pdb=" O GLU A 11 " -0.003 2.00e-02 2.50e+03 pdb=" N VAL A 12 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 11 " 0.002 2.00e-02 2.50e+03 3.93e-03 1.54e-01 pdb=" C GLU H 11 " -0.007 2.00e-02 2.50e+03 pdb=" O GLU H 11 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL H 12 " 0.002 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.70 - 3.14: 1818 3.14 - 3.58: 2519 3.58 - 4.02: 3858 4.02 - 4.46: 4130 4.46 - 4.90: 7188 Nonbonded interactions: 19513 Sorted by model distance: nonbonded pdb=" N ALA E 42 " pdb=" O ALA E 42 " model vdw 2.704 2.496 nonbonded pdb=" N ALA A 42 " pdb=" O ALA A 42 " model vdw 2.704 2.496 nonbonded pdb=" N ALA C 42 " pdb=" O ALA C 42 " model vdw 2.704 2.496 nonbonded pdb=" N ALA B 42 " pdb=" O ALA B 42 " model vdw 2.704 2.496 nonbonded pdb=" N GLY F 37 " pdb=" O GLY F 37 " model vdw 2.704 2.496 ... (remaining 19508 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: 0.01 Found NCS groups: ncs_group { reference = chain 'R' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.540 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.006 0.034 2550 Z= 0.262 Angle : 0.590 3.689 3430 Z= 0.356 Chirality : 0.064 0.147 390 Planarity : 0.001 0.004 440 Dihedral : 14.801 49.043 860 Min Nonbonded Distance : 2.704 Molprobity Statistics. All-atom Clashscore : 0.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.43), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.30 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR R 10 PHE 0.005 0.001 PHE D 19 HIS 0.003 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00641 ( 2550) covalent geometry : angle 0.58963 ( 3430) hydrogen bonds : bond 0.24288 ( 58) hydrogen bonds : angle 7.69016 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.093 Fit side-chains REVERT: R 11 GLU cc_start: 0.7278 (tt0) cc_final: 0.6928 (tt0) REVERT: R 28 LYS cc_start: 0.8024 (mttt) cc_final: 0.7712 (mtpp) REVERT: A 11 GLU cc_start: 0.7122 (tt0) cc_final: 0.6866 (tt0) REVERT: A 28 LYS cc_start: 0.7926 (mttt) cc_final: 0.7577 (mttp) REVERT: B 11 GLU cc_start: 0.7225 (tt0) cc_final: 0.6724 (tm-30) REVERT: B 16 LYS cc_start: 0.7879 (tttt) cc_final: 0.7604 (tttp) REVERT: B 28 LYS cc_start: 0.8219 (mttt) cc_final: 0.8010 (mttt) REVERT: C 28 LYS cc_start: 0.8231 (mttt) cc_final: 0.7835 (ttmt) REVERT: C 35 MET cc_start: 0.8673 (ttt) cc_final: 0.8414 (ttt) REVERT: F 26 SER cc_start: 0.8149 (t) cc_final: 0.7851 (m) REVERT: F 28 LYS cc_start: 0.8244 (mttt) cc_final: 0.7945 (mttt) REVERT: G 28 LYS cc_start: 0.8038 (mttt) cc_final: 0.7763 (ttmt) REVERT: H 22 GLU cc_start: 0.8043 (mm-30) cc_final: 0.6610 (mp0) REVERT: I 22 GLU cc_start: 0.8036 (mm-30) cc_final: 0.6064 (mp0) REVERT: I 26 SER cc_start: 0.8032 (t) cc_final: 0.7707 (m) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3836 time to fit residues: 22.3431 Evaluate side-chains 45 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.096502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077527 restraints weight = 2965.132| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.58 r_work: 0.3056 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2550 Z= 0.227 Angle : 0.649 6.577 3430 Z= 0.346 Chirality : 0.066 0.173 390 Planarity : 0.002 0.008 440 Dihedral : 6.018 24.639 350 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 4.40 % Allowed : 18.80 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.13 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 10 PHE 0.006 0.001 PHE F 19 HIS 0.003 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 2550) covalent geometry : angle 0.64933 ( 3430) hydrogen bonds : bond 0.03858 ( 58) hydrogen bonds : angle 5.85388 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.098 Fit side-chains REVERT: R 10 TYR cc_start: 0.7331 (m-80) cc_final: 0.7128 (m-80) REVERT: R 23 ASP cc_start: 0.6824 (m-30) cc_final: 0.6496 (m-30) REVERT: R 28 LYS cc_start: 0.7885 (mttt) cc_final: 0.7559 (mttp) REVERT: A 28 LYS cc_start: 0.7810 (mttt) cc_final: 0.7533 (mttp) REVERT: B 10 TYR cc_start: 0.7501 (m-80) cc_final: 0.6985 (m-80) REVERT: B 28 LYS cc_start: 0.8065 (mttt) cc_final: 0.7865 (mttt) REVERT: C 35 MET cc_start: 0.8537 (ttt) cc_final: 0.8269 (ttt) REVERT: E 16 LYS cc_start: 0.7974 (tttt) cc_final: 0.7642 (ttmm) REVERT: E 26 SER cc_start: 0.8783 (t) cc_final: 0.8357 (m) REVERT: F 15 GLN cc_start: 0.8784 (mp10) cc_final: 0.8501 (mp-120) REVERT: F 26 SER cc_start: 0.8063 (t) cc_final: 0.7721 (m) REVERT: F 28 LYS cc_start: 0.8097 (mttt) cc_final: 0.7801 (mttt) REVERT: F 34 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7718 (tt) REVERT: G 28 LYS cc_start: 0.8133 (mttt) cc_final: 0.7633 (mttm) REVERT: G 34 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7802 (tt) REVERT: I 16 LYS cc_start: 0.8310 (tttt) cc_final: 0.7552 (ttmp) REVERT: I 22 GLU cc_start: 0.8244 (mm-30) cc_final: 0.6046 (mt-10) REVERT: I 26 SER cc_start: 0.8420 (t) cc_final: 0.8000 (m) outliers start: 11 outliers final: 1 residues processed: 52 average time/residue: 0.5403 time to fit residues: 28.7130 Evaluate side-chains 47 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.097752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.079021 restraints weight = 3038.037| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.61 r_work: 0.3115 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2550 Z= 0.201 Angle : 0.602 5.954 3430 Z= 0.323 Chirality : 0.065 0.162 390 Planarity : 0.002 0.007 440 Dihedral : 6.074 28.015 350 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.40 % Allowed : 22.40 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 10 PHE 0.005 0.001 PHE I 20 HIS 0.003 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 2550) covalent geometry : angle 0.60212 ( 3430) hydrogen bonds : bond 0.03273 ( 58) hydrogen bonds : angle 5.67684 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.058 Fit side-chains REVERT: R 10 TYR cc_start: 0.7295 (m-80) cc_final: 0.7089 (m-80) REVERT: R 23 ASP cc_start: 0.6929 (m-30) cc_final: 0.6642 (m-30) REVERT: R 28 LYS cc_start: 0.7908 (mttt) cc_final: 0.7592 (mttp) REVERT: A 28 LYS cc_start: 0.7759 (mttt) cc_final: 0.7505 (mttp) REVERT: B 10 TYR cc_start: 0.7408 (m-80) cc_final: 0.7025 (m-80) REVERT: B 16 LYS cc_start: 0.7781 (tttt) cc_final: 0.7373 (tttp) REVERT: C 35 MET cc_start: 0.8583 (ttt) cc_final: 0.8285 (ttt) REVERT: E 16 LYS cc_start: 0.8287 (tttt) cc_final: 0.7957 (ttmm) REVERT: E 26 SER cc_start: 0.8834 (t) cc_final: 0.8419 (m) REVERT: F 15 GLN cc_start: 0.8790 (mp10) cc_final: 0.8464 (mp-120) REVERT: F 26 SER cc_start: 0.8003 (t) cc_final: 0.7742 (m) REVERT: F 28 LYS cc_start: 0.8116 (mttt) cc_final: 0.7812 (mttt) REVERT: F 34 LEU cc_start: 0.8077 (tp) cc_final: 0.7762 (tt) REVERT: G 28 LYS cc_start: 0.8170 (mttt) cc_final: 0.7680 (mttm) REVERT: G 34 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7791 (tt) REVERT: I 16 LYS cc_start: 0.8384 (tttt) cc_final: 0.7625 (ttmp) REVERT: I 22 GLU cc_start: 0.8227 (mm-30) cc_final: 0.6088 (mt-10) REVERT: I 26 SER cc_start: 0.8502 (t) cc_final: 0.8077 (m) outliers start: 6 outliers final: 1 residues processed: 50 average time/residue: 0.4893 time to fit residues: 24.9864 Evaluate side-chains 48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain G residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.0070 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 0.0270 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.4062 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.098515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.079715 restraints weight = 3020.421| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.60 r_work: 0.3212 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2550 Z= 0.165 Angle : 0.565 6.190 3430 Z= 0.305 Chirality : 0.064 0.153 390 Planarity : 0.002 0.006 440 Dihedral : 5.933 27.749 350 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.00 % Allowed : 22.40 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 10 PHE 0.004 0.001 PHE I 20 HIS 0.003 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 2550) covalent geometry : angle 0.56549 ( 3430) hydrogen bonds : bond 0.02960 ( 58) hydrogen bonds : angle 5.52583 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.059 Fit side-chains REVERT: R 10 TYR cc_start: 0.7334 (m-80) cc_final: 0.7067 (m-80) REVERT: R 23 ASP cc_start: 0.7058 (m-30) cc_final: 0.6778 (m-30) REVERT: R 28 LYS cc_start: 0.7998 (mttt) cc_final: 0.7709 (mttp) REVERT: B 10 TYR cc_start: 0.7569 (m-80) cc_final: 0.7213 (m-80) REVERT: B 16 LYS cc_start: 0.7879 (tttt) cc_final: 0.7467 (tttm) REVERT: C 35 MET cc_start: 0.8582 (ttt) cc_final: 0.8315 (ttt) REVERT: E 16 LYS cc_start: 0.8359 (tttt) cc_final: 0.8053 (ttmm) REVERT: E 26 SER cc_start: 0.8875 (t) cc_final: 0.8458 (m) REVERT: E 28 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7947 (mttt) REVERT: F 26 SER cc_start: 0.8126 (t) cc_final: 0.7815 (m) REVERT: F 28 LYS cc_start: 0.8170 (mttt) cc_final: 0.7879 (mttt) REVERT: F 34 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7844 (tt) REVERT: G 28 LYS cc_start: 0.8237 (mttt) cc_final: 0.7793 (mttm) REVERT: G 34 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7831 (tt) REVERT: H 28 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8059 (ttmt) REVERT: I 16 LYS cc_start: 0.8369 (tttt) cc_final: 0.7676 (ttmp) REVERT: I 22 GLU cc_start: 0.8302 (mm-30) cc_final: 0.6078 (mp0) REVERT: I 26 SER cc_start: 0.8453 (t) cc_final: 0.8030 (m) outliers start: 10 outliers final: 1 residues processed: 54 average time/residue: 0.4937 time to fit residues: 27.2720 Evaluate side-chains 48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.094828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.076239 restraints weight = 3093.616| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.62 r_work: 0.3155 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2550 Z= 0.251 Angle : 0.670 7.973 3430 Z= 0.350 Chirality : 0.067 0.163 390 Planarity : 0.002 0.007 440 Dihedral : 6.576 32.746 350 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.60 % Allowed : 20.80 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR E 10 PHE 0.006 0.002 PHE I 20 HIS 0.004 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00592 ( 2550) covalent geometry : angle 0.66986 ( 3430) hydrogen bonds : bond 0.03213 ( 58) hydrogen bonds : angle 5.47958 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.100 Fit side-chains REVERT: R 10 TYR cc_start: 0.7325 (m-80) cc_final: 0.7108 (m-80) REVERT: R 23 ASP cc_start: 0.7038 (m-30) cc_final: 0.6724 (m-30) REVERT: R 28 LYS cc_start: 0.7984 (mttt) cc_final: 0.7701 (mttp) REVERT: A 34 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7756 (tp) REVERT: B 10 TYR cc_start: 0.7556 (m-80) cc_final: 0.7278 (m-80) REVERT: B 16 LYS cc_start: 0.7895 (tttt) cc_final: 0.7508 (tttp) REVERT: B 34 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7963 (tp) REVERT: C 35 MET cc_start: 0.8546 (ttt) cc_final: 0.8291 (ttt) REVERT: E 16 LYS cc_start: 0.8414 (tttt) cc_final: 0.8070 (tttp) REVERT: E 26 SER cc_start: 0.8868 (t) cc_final: 0.8456 (m) REVERT: F 26 SER cc_start: 0.8012 (t) cc_final: 0.7803 (m) REVERT: F 28 LYS cc_start: 0.8141 (mttt) cc_final: 0.7853 (mttt) REVERT: F 34 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7892 (tt) REVERT: G 28 LYS cc_start: 0.8270 (mttt) cc_final: 0.7879 (mttm) REVERT: G 34 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7907 (tt) REVERT: H 17 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8017 (tt) REVERT: H 28 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8151 (ttmt) REVERT: I 16 LYS cc_start: 0.8377 (tttt) cc_final: 0.7680 (ttmp) REVERT: I 22 GLU cc_start: 0.8248 (mm-30) cc_final: 0.6116 (mt-10) REVERT: I 26 SER cc_start: 0.8507 (t) cc_final: 0.8109 (m) outliers start: 14 outliers final: 2 residues processed: 54 average time/residue: 0.5391 time to fit residues: 29.8176 Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.099762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081705 restraints weight = 2989.081| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.54 r_work: 0.3173 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2550 Z= 0.107 Angle : 0.499 5.112 3430 Z= 0.278 Chirality : 0.061 0.143 390 Planarity : 0.001 0.006 440 Dihedral : 5.606 25.977 350 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.20 % Allowed : 23.60 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 10 PHE 0.002 0.001 PHE G 20 HIS 0.002 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 2550) covalent geometry : angle 0.49850 ( 3430) hydrogen bonds : bond 0.02673 ( 58) hydrogen bonds : angle 5.34137 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.097 Fit side-chains REVERT: R 10 TYR cc_start: 0.7329 (m-80) cc_final: 0.6950 (m-80) REVERT: R 23 ASP cc_start: 0.7057 (m-30) cc_final: 0.6772 (m-30) REVERT: R 28 LYS cc_start: 0.7909 (mttt) cc_final: 0.7690 (mttp) REVERT: B 10 TYR cc_start: 0.7450 (m-80) cc_final: 0.7135 (m-80) REVERT: B 16 LYS cc_start: 0.7754 (tttt) cc_final: 0.7346 (tttp) REVERT: C 35 MET cc_start: 0.8523 (ttt) cc_final: 0.8230 (ttt) REVERT: D 41 ILE cc_start: 0.8351 (mm) cc_final: 0.8038 (mt) REVERT: E 16 LYS cc_start: 0.8209 (tttt) cc_final: 0.7839 (tttp) REVERT: E 26 SER cc_start: 0.8817 (t) cc_final: 0.8385 (m) REVERT: E 28 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7762 (mttt) REVERT: F 26 SER cc_start: 0.8006 (t) cc_final: 0.7667 (m) REVERT: F 28 LYS cc_start: 0.7988 (mttt) cc_final: 0.7690 (mttt) REVERT: F 34 LEU cc_start: 0.8084 (tp) cc_final: 0.7754 (tt) REVERT: G 28 LYS cc_start: 0.8101 (mttt) cc_final: 0.7677 (mttm) REVERT: H 11 GLU cc_start: 0.7734 (tt0) cc_final: 0.7462 (tt0) REVERT: I 16 LYS cc_start: 0.8363 (tttt) cc_final: 0.7635 (ttmp) REVERT: I 22 GLU cc_start: 0.8239 (mm-30) cc_final: 0.5936 (mp0) REVERT: I 26 SER cc_start: 0.8376 (t) cc_final: 0.7920 (m) outliers start: 8 outliers final: 1 residues processed: 51 average time/residue: 0.5343 time to fit residues: 27.9212 Evaluate side-chains 47 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.095340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.076856 restraints weight = 3060.063| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.58 r_work: 0.3070 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 2550 Z= 0.266 Angle : 0.686 8.226 3430 Z= 0.355 Chirality : 0.066 0.166 390 Planarity : 0.002 0.007 440 Dihedral : 6.670 32.386 350 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.80 % Allowed : 21.60 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 10 PHE 0.007 0.002 PHE A 20 HIS 0.005 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 2550) covalent geometry : angle 0.68557 ( 3430) hydrogen bonds : bond 0.03119 ( 58) hydrogen bonds : angle 5.35860 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.114 Fit side-chains REVERT: R 10 TYR cc_start: 0.7364 (m-80) cc_final: 0.7119 (m-80) REVERT: R 22 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7464 (mm-30) REVERT: R 23 ASP cc_start: 0.6943 (m-30) cc_final: 0.6706 (m-30) REVERT: R 28 LYS cc_start: 0.7905 (mttt) cc_final: 0.7612 (mttp) REVERT: A 34 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7716 (tp) REVERT: B 16 LYS cc_start: 0.7860 (tttt) cc_final: 0.7449 (tttp) REVERT: C 35 MET cc_start: 0.8523 (ttt) cc_final: 0.8264 (ttt) REVERT: D 41 ILE cc_start: 0.8389 (mm) cc_final: 0.8085 (mt) REVERT: E 16 LYS cc_start: 0.8283 (tttt) cc_final: 0.7894 (tttp) REVERT: E 26 SER cc_start: 0.8802 (t) cc_final: 0.8383 (m) REVERT: F 16 LYS cc_start: 0.7790 (tttt) cc_final: 0.7276 (mtpp) REVERT: F 26 SER cc_start: 0.7970 (t) cc_final: 0.7735 (m) REVERT: F 28 LYS cc_start: 0.8004 (mttt) cc_final: 0.7707 (mtpt) REVERT: F 34 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7878 (tt) REVERT: G 28 LYS cc_start: 0.8268 (mttt) cc_final: 0.7869 (mttm) REVERT: G 34 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7854 (tt) REVERT: I 16 LYS cc_start: 0.8382 (tttt) cc_final: 0.7647 (ttmp) REVERT: I 22 GLU cc_start: 0.8169 (mm-30) cc_final: 0.5966 (mt-10) REVERT: I 26 SER cc_start: 0.8430 (t) cc_final: 0.7997 (m) outliers start: 12 outliers final: 4 residues processed: 55 average time/residue: 0.5224 time to fit residues: 29.4470 Evaluate side-chains 54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.103925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085354 restraints weight = 2955.240| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.59 r_work: 0.3273 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2550 Z= 0.078 Angle : 0.458 5.169 3430 Z= 0.261 Chirality : 0.059 0.127 390 Planarity : 0.001 0.006 440 Dihedral : 5.237 21.915 350 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.40 % Allowed : 24.00 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR R 10 PHE 0.004 0.001 PHE R 19 HIS 0.002 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 2550) covalent geometry : angle 0.45759 ( 3430) hydrogen bonds : bond 0.02376 ( 58) hydrogen bonds : angle 5.34729 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.097 Fit side-chains REVERT: R 10 TYR cc_start: 0.7296 (m-80) cc_final: 0.6858 (m-80) REVERT: R 28 LYS cc_start: 0.8009 (mttt) cc_final: 0.7722 (mttp) REVERT: A 10 TYR cc_start: 0.7296 (m-80) cc_final: 0.6883 (m-80) REVERT: B 16 LYS cc_start: 0.7895 (tttt) cc_final: 0.7528 (tttp) REVERT: C 22 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7961 (mm-30) REVERT: C 35 MET cc_start: 0.8485 (ttt) cc_final: 0.8237 (ttt) REVERT: D 41 ILE cc_start: 0.8441 (mm) cc_final: 0.8078 (mt) REVERT: E 16 LYS cc_start: 0.8255 (tttt) cc_final: 0.8000 (ttmm) REVERT: E 26 SER cc_start: 0.8847 (t) cc_final: 0.8411 (m) REVERT: E 28 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7854 (mttt) REVERT: F 26 SER cc_start: 0.8019 (t) cc_final: 0.7695 (m) REVERT: F 28 LYS cc_start: 0.8136 (mttt) cc_final: 0.7802 (mttt) REVERT: G 28 LYS cc_start: 0.8179 (mttt) cc_final: 0.7698 (mttm) REVERT: H 11 GLU cc_start: 0.7683 (tt0) cc_final: 0.7365 (tt0) REVERT: I 16 LYS cc_start: 0.8323 (tttt) cc_final: 0.7613 (ttmp) REVERT: I 22 GLU cc_start: 0.8284 (mm-30) cc_final: 0.6112 (mt-10) REVERT: I 26 SER cc_start: 0.8398 (t) cc_final: 0.7903 (m) outliers start: 6 outliers final: 1 residues processed: 49 average time/residue: 0.5537 time to fit residues: 27.7371 Evaluate side-chains 45 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 0.0570 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.095378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.077098 restraints weight = 3144.061| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.63 r_work: 0.3134 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 2550 Z= 0.245 Angle : 0.671 6.607 3430 Z= 0.345 Chirality : 0.066 0.160 390 Planarity : 0.002 0.007 440 Dihedral : 6.436 29.157 350 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.60 % Allowed : 22.00 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR D 10 PHE 0.007 0.002 PHE A 20 HIS 0.004 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 2550) covalent geometry : angle 0.67127 ( 3430) hydrogen bonds : bond 0.02919 ( 58) hydrogen bonds : angle 5.46992 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.099 Fit side-chains REVERT: R 10 TYR cc_start: 0.7315 (m-80) cc_final: 0.6997 (m-80) REVERT: R 28 LYS cc_start: 0.8004 (mttt) cc_final: 0.7717 (mttp) REVERT: A 34 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7735 (tp) REVERT: B 16 LYS cc_start: 0.7875 (tttt) cc_final: 0.7477 (tttp) REVERT: C 22 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7962 (mm-30) REVERT: C 35 MET cc_start: 0.8536 (ttt) cc_final: 0.8312 (ttt) REVERT: D 41 ILE cc_start: 0.8403 (mm) cc_final: 0.8068 (mt) REVERT: E 16 LYS cc_start: 0.8369 (tttt) cc_final: 0.8011 (tttp) REVERT: E 26 SER cc_start: 0.8847 (t) cc_final: 0.8432 (m) REVERT: E 28 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7843 (mttt) REVERT: F 16 LYS cc_start: 0.7860 (tttt) cc_final: 0.7380 (mtpp) REVERT: F 26 SER cc_start: 0.7953 (t) cc_final: 0.7730 (m) REVERT: F 28 LYS cc_start: 0.8127 (mttt) cc_final: 0.7848 (mtpt) REVERT: F 34 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7785 (tt) REVERT: G 28 LYS cc_start: 0.8312 (mttt) cc_final: 0.7955 (mttm) REVERT: G 34 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7893 (tt) REVERT: H 11 GLU cc_start: 0.7816 (tt0) cc_final: 0.7553 (tt0) REVERT: H 28 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7819 (ttmt) REVERT: I 16 LYS cc_start: 0.8421 (tttt) cc_final: 0.7746 (ttmp) REVERT: I 22 GLU cc_start: 0.8204 (mm-30) cc_final: 0.6066 (mp0) REVERT: I 26 SER cc_start: 0.8467 (t) cc_final: 0.8036 (m) outliers start: 9 outliers final: 2 residues processed: 52 average time/residue: 0.5205 time to fit residues: 27.7032 Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.102569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084163 restraints weight = 2991.782| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.57 r_work: 0.3235 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2550 Z= 0.093 Angle : 0.485 5.451 3430 Z= 0.270 Chirality : 0.060 0.129 390 Planarity : 0.001 0.006 440 Dihedral : 5.411 22.780 350 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.20 % Allowed : 23.60 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 10 PHE 0.003 0.001 PHE R 19 HIS 0.002 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 2550) covalent geometry : angle 0.48488 ( 3430) hydrogen bonds : bond 0.02389 ( 58) hydrogen bonds : angle 5.38490 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.102 Fit side-chains REVERT: R 10 TYR cc_start: 0.7249 (m-80) cc_final: 0.7021 (m-80) REVERT: R 28 LYS cc_start: 0.7933 (mttt) cc_final: 0.7637 (mttp) REVERT: A 10 TYR cc_start: 0.7236 (m-80) cc_final: 0.6853 (m-80) REVERT: B 16 LYS cc_start: 0.7785 (tttt) cc_final: 0.7360 (tttp) REVERT: C 35 MET cc_start: 0.8545 (ttt) cc_final: 0.8284 (ttt) REVERT: D 41 ILE cc_start: 0.8376 (mm) cc_final: 0.8013 (mt) REVERT: E 16 LYS cc_start: 0.8223 (tttt) cc_final: 0.7863 (tttp) REVERT: E 26 SER cc_start: 0.8805 (t) cc_final: 0.8372 (m) REVERT: F 16 LYS cc_start: 0.7777 (tttt) cc_final: 0.7209 (mtpp) REVERT: F 26 SER cc_start: 0.7900 (t) cc_final: 0.7558 (m) REVERT: F 28 LYS cc_start: 0.8032 (mttt) cc_final: 0.7718 (mttt) REVERT: F 34 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7669 (tt) REVERT: G 28 LYS cc_start: 0.8182 (mttt) cc_final: 0.7794 (mttm) REVERT: H 11 GLU cc_start: 0.7718 (tt0) cc_final: 0.7380 (tt0) REVERT: I 16 LYS cc_start: 0.8330 (tttt) cc_final: 0.7602 (ttmp) REVERT: I 22 GLU cc_start: 0.8264 (mm-30) cc_final: 0.6111 (mt-10) REVERT: I 26 SER cc_start: 0.8385 (t) cc_final: 0.7892 (m) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.5785 time to fit residues: 26.6572 Evaluate side-chains 46 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.098533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080109 restraints weight = 3130.258| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.64 r_work: 0.3141 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2550 Z= 0.162 Angle : 0.593 7.476 3430 Z= 0.307 Chirality : 0.062 0.145 390 Planarity : 0.002 0.006 440 Dihedral : 5.901 25.968 350 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.00 % Allowed : 22.80 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR D 10 PHE 0.003 0.001 PHE G 20 HIS 0.003 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 2550) covalent geometry : angle 0.59269 ( 3430) hydrogen bonds : bond 0.02618 ( 58) hydrogen bonds : angle 5.40598 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 957.08 seconds wall clock time: 16 minutes 58.86 seconds (1018.86 seconds total)