Starting phenix.real_space_refine on Sun Mar 10 22:28:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff2_29036/03_2024/8ff2_29036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff2_29036/03_2024/8ff2_29036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff2_29036/03_2024/8ff2_29036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff2_29036/03_2024/8ff2_29036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff2_29036/03_2024/8ff2_29036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ff2_29036/03_2024/8ff2_29036.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 S 10 5.16 5 C 1840 2.51 5 N 510 2.21 5 O 550 1.98 5 H 2740 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5650 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Chain: "B" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Chain: "C" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Chain: "D" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Chain: "E" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Chain: "F" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Chain: "G" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Chain: "I" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Chain: "K" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Time building chain proxies: 2.87, per 1000 atoms: 0.51 Number of scatterers: 5650 At special positions: 0 Unit cell: (70.56, 90.72, 47.04, 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 10 16.00 O 550 8.00 N 510 7.00 C 1840 6.00 H 2740 1.00 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 - 3.50 Amino acid : False - 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: 3.67 Conformation dependent library (CDL) restraints added in 675.0 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 640 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21 removed outlier: 6.728A pdb=" N GLN A 15 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL C 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE C 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 19 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN C 15 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL E 18 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE E 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 19 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN E 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL G 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE G 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE E 19 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN G 15 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL J 18 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU G 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE J 20 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE G 19 " --> pdb=" O PHE J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 21 removed outlier: 6.728A pdb=" N GLN B 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL D 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE D 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 19 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN D 15 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL F 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE F 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE D 19 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN F 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL I 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU F 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE I 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE F 19 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN I 15 " --> pdb=" O LYS K 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL K 18 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU I 17 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE K 20 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE I 19 " --> pdb=" O PHE K 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 16 hydrogen bonds defined for protein. 48 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: 1.82 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2740 1.03 - 1.22: 0 1.22 - 1.42: 1360 1.42 - 1.61: 1590 1.61 - 1.80: 20 Bond restraints: 5710 Sorted by residual: bond pdb=" CA HIS G 6 " pdb=" C HIS G 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 8.17e-01 bond pdb=" CA HIS D 6 " pdb=" C HIS D 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 8.09e-01 bond pdb=" CA HIS K 6 " pdb=" C HIS K 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.98e-01 bond pdb=" CA HIS A 6 " pdb=" C HIS A 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.70e-01 bond pdb=" CA HIS C 6 " pdb=" C HIS C 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.51e-01 ... (remaining 5705 not shown) Histogram of bond angle deviations from ideal: 101.05 - 107.13: 63 107.13 - 113.21: 6367 113.21 - 119.29: 1161 119.29 - 125.37: 2427 125.37 - 131.45: 202 Bond angle restraints: 10220 Sorted by residual: angle pdb=" N GLY D 9 " pdb=" CA GLY D 9 " pdb=" C GLY D 9 " ideal model delta sigma weight residual 112.57 110.63 1.94 1.37e+00 5.33e-01 2.00e+00 angle pdb=" N GLY B 9 " pdb=" CA GLY B 9 " pdb=" C GLY B 9 " ideal model delta sigma weight residual 112.57 110.64 1.93 1.37e+00 5.33e-01 1.98e+00 angle pdb=" N GLY J 9 " pdb=" CA GLY J 9 " pdb=" C GLY J 9 " ideal model delta sigma weight residual 112.57 110.67 1.90 1.37e+00 5.33e-01 1.92e+00 angle pdb=" N GLY K 9 " pdb=" CA GLY K 9 " pdb=" C GLY K 9 " ideal model delta sigma weight residual 112.57 110.68 1.89 1.37e+00 5.33e-01 1.90e+00 angle pdb=" N GLY I 9 " pdb=" CA GLY I 9 " pdb=" C GLY I 9 " ideal model delta sigma weight residual 112.57 110.68 1.89 1.37e+00 5.33e-01 1.90e+00 ... (remaining 10215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.32: 2300 11.32 - 22.65: 200 22.65 - 33.97: 30 33.97 - 45.29: 60 45.29 - 56.61: 60 Dihedral angle restraints: 2650 sinusoidal: 1350 harmonic: 1300 Sorted by residual: dihedral pdb=" CA HIS K 13 " pdb=" C HIS K 13 " pdb=" N HIS K 14 " pdb=" CA HIS K 14 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA HIS I 13 " pdb=" C HIS I 13 " pdb=" N HIS I 14 " pdb=" CA HIS I 14 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA HIS A 13 " pdb=" C HIS A 13 " pdb=" N HIS A 14 " pdb=" CA HIS A 14 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 2647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 214 0.023 - 0.046: 126 0.046 - 0.069: 0 0.069 - 0.092: 10 0.092 - 0.115: 50 Chirality restraints: 400 Sorted by residual: chirality pdb=" CA VAL E 18 " pdb=" N VAL E 18 " pdb=" C VAL E 18 " pdb=" CB VAL E 18 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA VAL D 18 " pdb=" N VAL D 18 " pdb=" C VAL D 18 " pdb=" CB VAL D 18 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.22e-01 chirality pdb=" CA VAL G 18 " pdb=" N VAL G 18 " pdb=" C VAL G 18 " pdb=" CB VAL G 18 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 397 not shown) Planarity restraints: 900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 13 " 0.004 2.00e-02 2.50e+03 3.40e-03 2.60e-01 pdb=" CG HIS A 13 " -0.009 2.00e-02 2.50e+03 pdb=" ND1 HIS A 13 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 13 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 13 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 13 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS A 13 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS A 13 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS A 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 13 " -0.005 2.00e-02 2.50e+03 3.35e-03 2.52e-01 pdb=" CG HIS K 13 " 0.008 2.00e-02 2.50e+03 pdb=" ND1 HIS K 13 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 13 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS K 13 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS K 13 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS K 13 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS K 13 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS K 13 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 13 " 0.004 2.00e-02 2.50e+03 3.28e-03 2.43e-01 pdb=" CG HIS G 13 " -0.008 2.00e-02 2.50e+03 pdb=" ND1 HIS G 13 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS G 13 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS G 13 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS G 13 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS G 13 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS G 13 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS G 13 " 0.001 2.00e-02 2.50e+03 ... (remaining 897 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.37: 2123 2.37 - 2.93: 12418 2.93 - 3.49: 13179 3.49 - 4.04: 20019 4.04 - 4.60: 28533 Nonbonded interactions: 76272 Sorted by model distance: nonbonded pdb="HE22 GLN A 15 " pdb=" O VAL D 36 " model vdw 1.818 1.850 nonbonded pdb="HE22 GLN E 15 " pdb=" O VAL I 36 " model vdw 1.818 1.850 nonbonded pdb="HE22 GLN B 15 " pdb=" O VAL E 36 " model vdw 1.818 1.850 nonbonded pdb="HE22 GLN G 15 " pdb=" O VAL K 36 " model vdw 1.818 1.850 nonbonded pdb="HE22 GLN F 15 " pdb=" O VAL J 36 " model vdw 1.818 1.850 ... (remaining 76267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 7.440 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: 0.100 Extract box with map and model: 25.240 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.780 Find NCS groups from input model: 0.280 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:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.005 0.017 2970 Z= 0.319 Angle : 0.429 1.979 3970 Z= 0.265 Chirality : 0.044 0.115 400 Planarity : 0.002 0.009 530 Dihedral : 10.635 42.562 1020 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.01 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 13 PHE 0.006 0.001 PHE D 19 TYR 0.001 0.001 TYR K 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.6486 (mmp-170) REVERT: A 27 ASN cc_start: 0.8497 (m-40) cc_final: 0.8264 (m110) REVERT: B 3 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7504 (tp30) REVERT: B 5 ARG cc_start: 0.8454 (mtt-85) cc_final: 0.6673 (mmp-170) REVERT: C 5 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7657 (mtp85) REVERT: C 7 ASP cc_start: 0.8358 (m-30) cc_final: 0.8157 (m-30) REVERT: C 27 ASN cc_start: 0.8597 (m-40) cc_final: 0.8370 (m-40) REVERT: D 11 GLU cc_start: 0.8388 (pt0) cc_final: 0.8003 (pt0) REVERT: F 5 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.8087 (tpp80) REVERT: F 13 HIS cc_start: 0.7885 (m90) cc_final: 0.7644 (m-70) REVERT: G 28 LYS cc_start: 0.8975 (tttt) cc_final: 0.8657 (tttm) REVERT: I 8 SER cc_start: 0.8898 (m) cc_final: 0.8548 (m) REVERT: I 11 GLU cc_start: 0.8275 (pt0) cc_final: 0.7988 (pt0) REVERT: I 28 LYS cc_start: 0.9122 (tttt) cc_final: 0.8849 (tttm) REVERT: J 5 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.5872 (ppt170) REVERT: J 28 LYS cc_start: 0.9081 (tttt) cc_final: 0.8160 (tppt) REVERT: K 5 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.6282 (pmt170) REVERT: K 11 GLU cc_start: 0.8203 (pt0) cc_final: 0.7920 (pt0) REVERT: K 28 LYS cc_start: 0.8996 (tttt) cc_final: 0.8220 (tppt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 2.1750 time to fit residues: 283.3603 Evaluate side-chains 108 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2970 Z= 0.320 Angle : 0.508 4.157 3970 Z= 0.294 Chirality : 0.051 0.148 400 Planarity : 0.002 0.012 530 Dihedral : 6.320 21.238 390 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.79 % Allowed : 15.52 % Favored : 80.69 % 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: -1.99 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 13 PHE 0.006 0.001 PHE J 19 TYR 0.012 0.001 TYR I 10 ARG 0.001 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.6495 (mmp-170) REVERT: A 28 LYS cc_start: 0.9258 (tttt) cc_final: 0.8962 (tttm) REVERT: B 5 ARG cc_start: 0.8418 (mtt-85) cc_final: 0.6798 (mmp-170) REVERT: C 5 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7962 (mtp85) REVERT: F 5 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.8205 (tpp80) REVERT: G 3 GLU cc_start: 0.7758 (mp0) cc_final: 0.7553 (mp0) REVERT: I 1 ASP cc_start: 0.7842 (p0) cc_final: 0.7585 (p0) REVERT: I 8 SER cc_start: 0.8748 (m) cc_final: 0.8307 (m) REVERT: I 28 LYS cc_start: 0.9149 (tttt) cc_final: 0.8839 (tttm) REVERT: J 5 ARG cc_start: 0.8461 (mtt-85) cc_final: 0.6052 (ppt170) REVERT: J 8 SER cc_start: 0.9046 (m) cc_final: 0.8789 (t) REVERT: J 10 TYR cc_start: 0.8428 (t80) cc_final: 0.7861 (t80) REVERT: J 11 GLU cc_start: 0.7983 (pt0) cc_final: 0.7470 (mm-30) REVERT: J 28 LYS cc_start: 0.9113 (tttt) cc_final: 0.8194 (tppt) REVERT: K 5 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.6413 (pmt170) REVERT: K 28 LYS cc_start: 0.8994 (tttt) cc_final: 0.8193 (tppt) outliers start: 11 outliers final: 3 residues processed: 117 average time/residue: 2.4357 time to fit residues: 291.6793 Evaluate side-chains 111 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 1 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN C 15 GLN G 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2970 Z= 0.274 Angle : 0.471 3.538 3970 Z= 0.274 Chirality : 0.049 0.135 400 Planarity : 0.002 0.014 530 Dihedral : 6.074 20.132 390 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.17 % Allowed : 16.55 % Favored : 78.28 % 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: -1.99 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 13 PHE 0.005 0.001 PHE J 19 TYR 0.012 0.002 TYR G 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.6465 (mmp-170) REVERT: A 28 LYS cc_start: 0.9259 (tttt) cc_final: 0.8995 (tttp) REVERT: B 5 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.6719 (mmp-170) REVERT: C 5 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.7838 (mtp85) REVERT: D 11 GLU cc_start: 0.8155 (pt0) cc_final: 0.7579 (pt0) REVERT: E 7 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8231 (m-30) REVERT: E 8 SER cc_start: 0.8559 (m) cc_final: 0.7613 (t) REVERT: E 11 GLU cc_start: 0.8294 (pt0) cc_final: 0.7818 (pt0) REVERT: E 28 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8667 (ttpt) REVERT: I 11 GLU cc_start: 0.8347 (pt0) cc_final: 0.8109 (pt0) REVERT: I 28 LYS cc_start: 0.9151 (tttt) cc_final: 0.8859 (tttm) REVERT: J 5 ARG cc_start: 0.8464 (mtt-85) cc_final: 0.6066 (ppt170) REVERT: J 8 SER cc_start: 0.9004 (m) cc_final: 0.8771 (t) REVERT: J 10 TYR cc_start: 0.8439 (t80) cc_final: 0.7884 (t80) REVERT: J 11 GLU cc_start: 0.7900 (pt0) cc_final: 0.7652 (mm-30) REVERT: J 28 LYS cc_start: 0.9112 (tttt) cc_final: 0.8201 (tppt) REVERT: K 5 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.6400 (pmt170) REVERT: K 28 LYS cc_start: 0.9022 (tttt) cc_final: 0.8247 (tppt) outliers start: 15 outliers final: 12 residues processed: 110 average time/residue: 2.3972 time to fit residues: 269.9300 Evaluate side-chains 118 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.0010 chunk 7 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2970 Z= 0.253 Angle : 0.471 3.646 3970 Z= 0.271 Chirality : 0.049 0.137 400 Planarity : 0.002 0.023 530 Dihedral : 5.850 18.697 390 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.45 % Allowed : 20.69 % Favored : 75.86 % 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: -1.87 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 13 PHE 0.003 0.001 PHE J 19 TYR 0.007 0.001 TYR I 10 ARG 0.001 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.6311 (mmp-170) REVERT: A 28 LYS cc_start: 0.9250 (tttt) cc_final: 0.8989 (tttp) REVERT: B 5 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.6461 (mmp-170) REVERT: C 5 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7855 (mtp85) REVERT: C 8 SER cc_start: 0.8754 (m) cc_final: 0.8350 (t) REVERT: D 11 GLU cc_start: 0.8116 (pt0) cc_final: 0.7580 (pt0) REVERT: E 7 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: E 8 SER cc_start: 0.8521 (m) cc_final: 0.7469 (t) REVERT: E 11 GLU cc_start: 0.8294 (pt0) cc_final: 0.7729 (pt0) REVERT: E 28 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8644 (ttpt) REVERT: F 15 GLN cc_start: 0.8559 (pt0) cc_final: 0.8356 (pt0) REVERT: G 3 GLU cc_start: 0.7748 (mp0) cc_final: 0.7541 (mp0) REVERT: I 11 GLU cc_start: 0.8216 (pt0) cc_final: 0.7984 (pt0) REVERT: I 28 LYS cc_start: 0.9140 (tttt) cc_final: 0.8810 (tttp) REVERT: J 5 ARG cc_start: 0.8492 (mtt-85) cc_final: 0.6147 (ppt170) REVERT: J 8 SER cc_start: 0.8909 (m) cc_final: 0.8703 (t) REVERT: J 10 TYR cc_start: 0.8455 (t80) cc_final: 0.8194 (t80) REVERT: J 28 LYS cc_start: 0.9110 (tttt) cc_final: 0.8201 (tppt) REVERT: K 1 ASP cc_start: 0.8263 (p0) cc_final: 0.7834 (p0) REVERT: K 5 ARG cc_start: 0.8582 (mtt-85) cc_final: 0.6338 (pmt170) REVERT: K 28 LYS cc_start: 0.9018 (tttt) cc_final: 0.8260 (tppt) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 2.2829 time to fit residues: 252.8200 Evaluate side-chains 112 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain I residue 1 ASP Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 26 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2970 Z= 0.247 Angle : 0.470 3.911 3970 Z= 0.268 Chirality : 0.049 0.137 400 Planarity : 0.002 0.013 530 Dihedral : 5.714 18.530 390 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.48 % Allowed : 22.07 % Favored : 73.45 % 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: -1.87 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 13 PHE 0.004 0.001 PHE B 4 TYR 0.013 0.001 TYR I 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.6271 (mmp-170) REVERT: A 28 LYS cc_start: 0.9251 (tttt) cc_final: 0.8980 (tttp) REVERT: C 5 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7857 (mtp85) REVERT: D 11 GLU cc_start: 0.8101 (pt0) cc_final: 0.7610 (pt0) REVERT: E 7 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8217 (m-30) REVERT: E 8 SER cc_start: 0.8632 (m) cc_final: 0.7661 (t) REVERT: E 11 GLU cc_start: 0.8248 (pt0) cc_final: 0.7682 (pt0) REVERT: E 28 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8664 (ttpt) REVERT: F 23 ASP cc_start: 0.7745 (m-30) cc_final: 0.7442 (m-30) REVERT: I 8 SER cc_start: 0.8762 (m) cc_final: 0.7838 (m) REVERT: I 11 GLU cc_start: 0.8031 (pt0) cc_final: 0.7691 (pt0) REVERT: I 28 LYS cc_start: 0.9145 (tttt) cc_final: 0.8809 (tttm) REVERT: J 5 ARG cc_start: 0.8457 (mtt-85) cc_final: 0.6132 (ppt170) REVERT: J 8 SER cc_start: 0.8895 (m) cc_final: 0.8653 (t) REVERT: J 28 LYS cc_start: 0.9106 (tttt) cc_final: 0.8198 (tppt) REVERT: K 1 ASP cc_start: 0.8227 (p0) cc_final: 0.7826 (p0) REVERT: K 5 ARG cc_start: 0.8602 (mtt-85) cc_final: 0.6317 (pmt170) REVERT: K 28 LYS cc_start: 0.9023 (tttt) cc_final: 0.8264 (tppt) outliers start: 13 outliers final: 10 residues processed: 107 average time/residue: 2.2301 time to fit residues: 244.8459 Evaluate side-chains 115 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 1 ASP Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2970 Z= 0.257 Angle : 0.485 5.050 3970 Z= 0.277 Chirality : 0.050 0.137 400 Planarity : 0.001 0.011 530 Dihedral : 5.650 18.375 390 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.83 % Allowed : 23.45 % Favored : 71.72 % 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: -1.91 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 13 PHE 0.004 0.001 PHE A 4 TYR 0.012 0.001 TYR I 10 ARG 0.002 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.6250 (mmp-170) REVERT: A 28 LYS cc_start: 0.9254 (tttt) cc_final: 0.8981 (tttp) REVERT: C 5 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7777 (mtp85) REVERT: D 11 GLU cc_start: 0.8100 (pt0) cc_final: 0.7579 (pt0) REVERT: E 7 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8229 (m-30) REVERT: E 8 SER cc_start: 0.8586 (m) cc_final: 0.7631 (t) REVERT: E 11 GLU cc_start: 0.8196 (pt0) cc_final: 0.7575 (pt0) REVERT: F 11 GLU cc_start: 0.8106 (pt0) cc_final: 0.7894 (pt0) REVERT: F 23 ASP cc_start: 0.7771 (m-30) cc_final: 0.7444 (m-30) REVERT: G 3 GLU cc_start: 0.7682 (mp0) cc_final: 0.7476 (mp0) REVERT: I 23 ASP cc_start: 0.7750 (m-30) cc_final: 0.7548 (m-30) REVERT: I 28 LYS cc_start: 0.9143 (tttt) cc_final: 0.8827 (tttm) REVERT: J 5 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.6164 (ppt170) REVERT: J 8 SER cc_start: 0.8872 (m) cc_final: 0.8638 (t) REVERT: J 28 LYS cc_start: 0.9104 (tttt) cc_final: 0.8195 (tppt) REVERT: K 5 ARG cc_start: 0.8605 (mtt-85) cc_final: 0.6298 (pmt170) REVERT: K 28 LYS cc_start: 0.9025 (tttt) cc_final: 0.8266 (tppt) outliers start: 14 outliers final: 10 residues processed: 107 average time/residue: 2.2933 time to fit residues: 251.5737 Evaluate side-chains 115 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.0270 chunk 19 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2970 Z= 0.260 Angle : 0.481 3.930 3970 Z= 0.274 Chirality : 0.049 0.145 400 Planarity : 0.001 0.010 530 Dihedral : 5.654 18.028 390 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.17 % Allowed : 24.48 % Favored : 70.34 % 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: -1.97 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 13 PHE 0.006 0.001 PHE A 4 TYR 0.013 0.001 TYR I 10 ARG 0.002 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.6345 (mmp-170) REVERT: A 28 LYS cc_start: 0.9253 (tttt) cc_final: 0.8981 (tttp) REVERT: D 11 GLU cc_start: 0.8077 (pt0) cc_final: 0.7584 (pt0) REVERT: E 7 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: E 8 SER cc_start: 0.8531 (m) cc_final: 0.7578 (t) REVERT: E 11 GLU cc_start: 0.8187 (pt0) cc_final: 0.7592 (pt0) REVERT: F 23 ASP cc_start: 0.7748 (m-30) cc_final: 0.7520 (m-30) REVERT: I 28 LYS cc_start: 0.9143 (tttt) cc_final: 0.8826 (tttm) REVERT: J 5 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.6157 (ppt170) REVERT: J 8 SER cc_start: 0.8875 (m) cc_final: 0.8637 (t) REVERT: J 28 LYS cc_start: 0.9101 (tttt) cc_final: 0.8193 (tppt) REVERT: K 5 ARG cc_start: 0.8603 (mtt-85) cc_final: 0.6271 (pmt170) REVERT: K 28 LYS cc_start: 0.9026 (tttt) cc_final: 0.8268 (tppt) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 2.1257 time to fit residues: 229.2097 Evaluate side-chains 114 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN G 15 GLN ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2970 Z= 0.252 Angle : 0.487 4.940 3970 Z= 0.278 Chirality : 0.049 0.135 400 Planarity : 0.001 0.009 530 Dihedral : 5.602 18.605 390 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.14 % Allowed : 25.86 % Favored : 70.00 % 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: -2.06 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 13 PHE 0.006 0.001 PHE A 4 TYR 0.012 0.001 TYR I 10 ARG 0.002 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.6332 (mmp-170) REVERT: A 28 LYS cc_start: 0.9253 (tttt) cc_final: 0.8993 (tttp) REVERT: D 11 GLU cc_start: 0.8050 (pt0) cc_final: 0.7503 (pt0) REVERT: E 3 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6805 (tm-30) REVERT: E 8 SER cc_start: 0.8533 (m) cc_final: 0.7603 (t) REVERT: E 11 GLU cc_start: 0.8184 (pt0) cc_final: 0.7570 (pt0) REVERT: E 28 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8675 (ttpt) REVERT: I 28 LYS cc_start: 0.9140 (tttt) cc_final: 0.8818 (tttp) REVERT: J 5 ARG cc_start: 0.8429 (mtt-85) cc_final: 0.6160 (ppt170) REVERT: J 8 SER cc_start: 0.8872 (m) cc_final: 0.8443 (t) REVERT: J 13 HIS cc_start: 0.6412 (OUTLIER) cc_final: 0.5965 (m170) REVERT: J 28 LYS cc_start: 0.9100 (tttt) cc_final: 0.8193 (tppt) REVERT: K 5 ARG cc_start: 0.8605 (mtt-85) cc_final: 0.6272 (pmt170) REVERT: K 28 LYS cc_start: 0.9026 (tttt) cc_final: 0.8268 (tppt) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 2.1968 time to fit residues: 229.9528 Evaluate side-chains 112 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain K residue 1 ASP Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN F 15 GLN G 15 GLN ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2970 Z= 0.322 Angle : 0.507 4.953 3970 Z= 0.291 Chirality : 0.050 0.135 400 Planarity : 0.002 0.010 530 Dihedral : 5.786 18.672 390 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.79 % Allowed : 27.24 % Favored : 68.97 % 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: -2.22 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 13 PHE 0.007 0.001 PHE A 4 TYR 0.013 0.001 TYR I 10 ARG 0.002 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9265 (tttt) cc_final: 0.9000 (tttp) REVERT: C 8 SER cc_start: 0.8906 (m) cc_final: 0.8495 (p) REVERT: C 10 TYR cc_start: 0.8374 (t80) cc_final: 0.8097 (t80) REVERT: D 11 GLU cc_start: 0.8091 (pt0) cc_final: 0.7653 (pt0) REVERT: E 3 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6745 (tm-30) REVERT: E 8 SER cc_start: 0.8419 (m) cc_final: 0.7463 (t) REVERT: E 11 GLU cc_start: 0.8180 (pt0) cc_final: 0.7651 (pt0) REVERT: F 23 ASP cc_start: 0.7848 (m-30) cc_final: 0.7543 (m-30) REVERT: I 28 LYS cc_start: 0.9146 (tttt) cc_final: 0.8819 (tttm) REVERT: J 5 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.6163 (ppt170) REVERT: J 28 LYS cc_start: 0.9108 (tttt) cc_final: 0.8199 (tppt) REVERT: K 5 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.6290 (pmt170) REVERT: K 28 LYS cc_start: 0.9032 (tttt) cc_final: 0.8267 (tppt) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 2.1326 time to fit residues: 227.8021 Evaluate side-chains 112 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN G 15 GLN ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2970 Z= 0.378 Angle : 0.523 4.304 3970 Z= 0.303 Chirality : 0.050 0.135 400 Planarity : 0.002 0.013 530 Dihedral : 5.948 19.719 390 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.79 % Allowed : 28.97 % Favored : 67.24 % 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: -2.47 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 13 PHE 0.008 0.001 PHE A 4 TYR 0.014 0.002 TYR I 10 ARG 0.001 0.000 ARG G 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9271 (tttt) cc_final: 0.9006 (tttp) REVERT: C 8 SER cc_start: 0.8901 (m) cc_final: 0.8527 (p) REVERT: C 10 TYR cc_start: 0.8400 (t80) cc_final: 0.8186 (t80) REVERT: D 11 GLU cc_start: 0.8122 (pt0) cc_final: 0.7598 (pt0) REVERT: E 8 SER cc_start: 0.8466 (m) cc_final: 0.7948 (t) REVERT: F 23 ASP cc_start: 0.7828 (m-30) cc_final: 0.7582 (m-30) REVERT: I 28 LYS cc_start: 0.9138 (tttt) cc_final: 0.8827 (tttm) REVERT: J 5 ARG cc_start: 0.8431 (mtt-85) cc_final: 0.6173 (ppt170) REVERT: J 28 LYS cc_start: 0.9113 (tttt) cc_final: 0.8201 (tppt) REVERT: K 5 ARG cc_start: 0.8599 (mtt-85) cc_final: 0.6348 (pmt170) REVERT: K 28 LYS cc_start: 0.9033 (tttt) cc_final: 0.8252 (tppt) outliers start: 11 outliers final: 9 residues processed: 103 average time/residue: 2.1232 time to fit residues: 224.5508 Evaluate side-chains 109 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN G 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.098301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.090044 restraints weight = 14439.739| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.58 r_work: 0.3595 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2970 Z= 0.398 Angle : 0.547 5.260 3970 Z= 0.316 Chirality : 0.049 0.140 400 Planarity : 0.002 0.011 530 Dihedral : 6.029 21.396 390 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.14 % Allowed : 28.62 % Favored : 67.24 % 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: -2.65 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 13 PHE 0.007 0.001 PHE A 4 TYR 0.014 0.001 TYR I 10 ARG 0.002 0.000 ARG D 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5464.17 seconds wall clock time: 95 minutes 45.18 seconds (5745.18 seconds total)