Starting phenix.real_space_refine on Wed Nov 13 23:46:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olo_16960/11_2024/8olo_16960.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olo_16960/11_2024/8olo_16960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olo_16960/11_2024/8olo_16960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olo_16960/11_2024/8olo_16960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olo_16960/11_2024/8olo_16960.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olo_16960/11_2024/8olo_16960.cif" } resolution = 3.5 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= -0.000 sd= 1.001 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 1520 2.51 5 N 390 2.21 5 O 410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2330 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 233 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.49, per 1000 atoms: 0.64 Number of scatterers: 2330 At special positions: 0 Unit cell: (92.92, 50.904, 40.4, 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 410 8.00 N 390 7.00 C 1520 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: 0.50 Conformation dependent library (CDL) restraints added in 266.9 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 54.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 20 removed outlier: 9.105A pdb=" N GLU A 11 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N HIS C 14 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A 13 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LYS C 16 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN A 15 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N PHE C 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 19 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU C 22 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 20 removed outlier: 9.105A pdb=" N GLU A 11 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N HIS C 14 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A 13 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LYS C 16 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN A 15 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N PHE C 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 19 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU C 22 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN E 15 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS C 16 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU E 17 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C 18 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE E 19 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE C 20 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA E 21 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU C 22 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN G 15 " --> pdb=" O HIS E 14 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS E 16 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU G 17 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 18 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE G 19 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE E 20 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA G 21 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU E 22 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN I 15 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS G 16 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU I 17 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL G 18 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE I 19 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE G 20 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA I 21 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU G 22 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.124A pdb=" N ILE C 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE E 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE G 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 24 removed outlier: 6.368A pdb=" N GLU D 11 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N HIS B 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N HIS D 13 " --> pdb=" O HIS B 14 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LYS B 16 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N GLN D 15 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N VAL B 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N LEU D 17 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N PHE B 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N PHE D 19 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N GLU B 22 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ALA D 21 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL B 24 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP D 23 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLN F 15 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS D 16 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU F 17 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 18 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE F 19 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE D 20 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA F 21 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU D 22 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN H 15 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS F 16 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU H 17 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL F 18 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE H 19 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE F 20 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA H 21 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU F 22 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL J 12 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS H 13 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS J 14 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP H 23 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL J 24 " --> pdb=" O ASP H 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.110A pdb=" N ILE D 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE F 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) 40 hydrogen bonds defined for protein. 120 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: 0.46 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 515 1.33 - 1.45: 518 1.45 - 1.56: 1317 1.56 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 2370 Sorted by residual: bond pdb=" C VAL H 12 " pdb=" O VAL H 12 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.13e-02 7.83e+03 6.15e+00 bond pdb=" C VAL I 12 " pdb=" O VAL I 12 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.13e-02 7.83e+03 6.13e+00 bond pdb=" C VAL C 12 " pdb=" O VAL C 12 " ideal model delta sigma weight residual 1.237 1.210 0.028 1.13e-02 7.83e+03 6.06e+00 bond pdb=" C VAL F 12 " pdb=" O VAL F 12 " ideal model delta sigma weight residual 1.237 1.210 0.028 1.13e-02 7.83e+03 5.96e+00 bond pdb=" C VAL D 12 " pdb=" O VAL D 12 " ideal model delta sigma weight residual 1.237 1.210 0.028 1.13e-02 7.83e+03 5.96e+00 ... (remaining 2365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 2961 1.42 - 2.84: 184 2.84 - 4.26: 15 4.26 - 5.68: 0 5.68 - 7.09: 20 Bond angle restraints: 3180 Sorted by residual: angle pdb=" C HIS I 14 " pdb=" N GLN I 15 " pdb=" CA GLN I 15 " ideal model delta sigma weight residual 122.95 130.04 -7.09 1.44e+00 4.82e-01 2.43e+01 angle pdb=" C HIS D 14 " pdb=" N GLN D 15 " pdb=" CA GLN D 15 " ideal model delta sigma weight residual 122.95 130.04 -7.09 1.44e+00 4.82e-01 2.42e+01 angle pdb=" C HIS E 14 " pdb=" N GLN E 15 " pdb=" CA GLN E 15 " ideal model delta sigma weight residual 122.95 130.02 -7.07 1.44e+00 4.82e-01 2.41e+01 angle pdb=" C HIS F 14 " pdb=" N GLN F 15 " pdb=" CA GLN F 15 " ideal model delta sigma weight residual 122.95 130.02 -7.07 1.44e+00 4.82e-01 2.41e+01 angle pdb=" C HIS C 14 " pdb=" N GLN C 15 " pdb=" CA GLN C 15 " ideal model delta sigma weight residual 122.95 130.02 -7.07 1.44e+00 4.82e-01 2.41e+01 ... (remaining 3175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.15: 1100 10.15 - 20.30: 148 20.30 - 30.46: 52 30.46 - 40.61: 10 40.61 - 50.76: 10 Dihedral angle restraints: 1320 sinusoidal: 490 harmonic: 830 Sorted by residual: dihedral pdb=" CA ALA J 21 " pdb=" C ALA J 21 " pdb=" N GLU J 22 " pdb=" CA GLU J 22 " ideal model delta harmonic sigma weight residual 180.00 -164.52 -15.48 0 5.00e+00 4.00e-02 9.58e+00 dihedral pdb=" CA ALA G 21 " pdb=" C ALA G 21 " pdb=" N GLU G 22 " pdb=" CA GLU G 22 " ideal model delta harmonic sigma weight residual -180.00 -164.55 -15.45 0 5.00e+00 4.00e-02 9.55e+00 dihedral pdb=" CA ALA C 21 " pdb=" C ALA C 21 " pdb=" N GLU C 22 " pdb=" CA GLU C 22 " ideal model delta harmonic sigma weight residual 180.00 -164.57 -15.43 0 5.00e+00 4.00e-02 9.52e+00 ... (remaining 1317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 223 0.040 - 0.080: 57 0.080 - 0.120: 40 0.120 - 0.160: 20 0.160 - 0.200: 20 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA VAL J 12 " pdb=" N VAL J 12 " pdb=" C VAL J 12 " pdb=" CB VAL J 12 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA VAL F 12 " pdb=" N VAL F 12 " pdb=" C VAL F 12 " pdb=" CB VAL F 12 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA VAL D 12 " pdb=" N VAL D 12 " pdb=" C VAL D 12 " pdb=" CB VAL D 12 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 357 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 11 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C GLU H 11 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU H 11 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL H 12 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 11 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C GLU J 11 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU J 11 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL J 12 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 11 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C GLU B 11 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU B 11 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL B 12 " 0.016 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 772 2.88 - 3.39: 1905 3.39 - 3.89: 3892 3.89 - 4.40: 4079 4.40 - 4.90: 7896 Nonbonded interactions: 18544 Sorted by model distance: nonbonded pdb=" N HIS H 14 " pdb=" O HIS J 14 " model vdw 2.375 3.120 nonbonded pdb=" OG SER C 26 " pdb=" O SER E 26 " model vdw 2.426 3.040 nonbonded pdb=" O TYR H 10 " pdb=" O GLU J 11 " model vdw 2.443 3.040 nonbonded pdb=" OG SER D 26 " pdb=" O SER F 26 " model vdw 2.473 3.040 nonbonded pdb=" O ASN A 27 " pdb=" N LYS C 28 " model vdw 2.480 3.120 ... (remaining 18539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 1.120 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.680 Find NCS groups from input model: 0.090 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.031 2370 Z= 0.349 Angle : 0.869 7.094 3180 Z= 0.559 Chirality : 0.072 0.200 360 Planarity : 0.005 0.027 400 Dihedral : 11.692 50.761 800 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 14 PHE 0.007 0.001 PHE C 20 TYR 0.004 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.267 Fit side-chains REVERT: B 32 ILE cc_start: 0.8195 (mt) cc_final: 0.7841 (mm) REVERT: G 10 TYR cc_start: 0.7448 (m-80) cc_final: 0.7196 (m-80) REVERT: H 11 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7254 (mt-10) REVERT: I 27 ASN cc_start: 0.5978 (t0) cc_final: 0.5684 (t0) REVERT: J 32 ILE cc_start: 0.7882 (mt) cc_final: 0.7434 (mm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0991 time to fit residues: 6.8538 Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS D 14 HIS B 14 HIS C 14 HIS E 14 HIS F 14 HIS G 14 HIS G 27 ASN H 14 HIS I 14 HIS J 14 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2370 Z= 0.274 Angle : 0.631 5.358 3180 Z= 0.346 Chirality : 0.057 0.140 360 Planarity : 0.002 0.014 400 Dihedral : 5.180 14.101 310 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.08 % Allowed : 12.08 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 13 PHE 0.007 0.001 PHE J 20 TYR 0.007 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.267 Fit side-chains REVERT: H 11 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7219 (mt-10) outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.0981 time to fit residues: 8.8617 Evaluate side-chains 72 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain I residue 35 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2370 Z= 0.366 Angle : 0.698 5.818 3180 Z= 0.380 Chirality : 0.058 0.142 360 Planarity : 0.002 0.010 400 Dihedral : 5.368 15.639 310 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.08 % Allowed : 17.08 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.38), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 13 PHE 0.007 0.001 PHE J 20 TYR 0.005 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.256 Fit side-chains REVERT: H 11 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7418 (mt-10) REVERT: J 35 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.6159 (tpt) outliers start: 5 outliers final: 2 residues processed: 74 average time/residue: 0.0944 time to fit residues: 8.8954 Evaluate side-chains 77 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2370 Z= 0.401 Angle : 0.691 5.170 3180 Z= 0.378 Chirality : 0.058 0.143 360 Planarity : 0.003 0.009 400 Dihedral : 5.485 15.280 310 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.33 % Allowed : 18.75 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.37), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 13 PHE 0.006 0.001 PHE J 20 TYR 0.005 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.255 Fit side-chains REVERT: J 35 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7324 (ppp) outliers start: 8 outliers final: 5 residues processed: 77 average time/residue: 0.0913 time to fit residues: 8.9627 Evaluate side-chains 80 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 2370 Z= 0.446 Angle : 0.744 5.478 3180 Z= 0.407 Chirality : 0.058 0.140 360 Planarity : 0.003 0.015 400 Dihedral : 5.880 16.642 310 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.83 % Allowed : 16.67 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.37), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 14 PHE 0.005 0.001 PHE J 20 TYR 0.008 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.265 Fit side-chains REVERT: H 10 TYR cc_start: 0.7562 (m-80) cc_final: 0.7350 (m-80) REVERT: I 10 TYR cc_start: 0.7623 (m-80) cc_final: 0.7280 (m-80) REVERT: J 35 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.5950 (tpt) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.0876 time to fit residues: 8.3984 Evaluate side-chains 79 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2370 Z= 0.297 Angle : 0.673 7.248 3180 Z= 0.359 Chirality : 0.056 0.134 360 Planarity : 0.002 0.012 400 Dihedral : 5.744 15.698 310 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.00 % Allowed : 17.08 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.38), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 13 PHE 0.003 0.001 PHE C 19 TYR 0.006 0.001 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.255 Fit side-chains REVERT: D 11 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7376 (mt-10) REVERT: B 15 GLN cc_start: 0.8715 (pm20) cc_final: 0.8414 (pm20) REVERT: H 10 TYR cc_start: 0.7606 (m-80) cc_final: 0.7384 (m-80) REVERT: J 35 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7222 (ppp) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.0882 time to fit residues: 8.6479 Evaluate side-chains 82 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2370 Z= 0.266 Angle : 0.648 6.871 3180 Z= 0.344 Chirality : 0.056 0.135 360 Planarity : 0.002 0.012 400 Dihedral : 5.647 15.586 310 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.58 % Allowed : 18.33 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.39), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.30), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 13 PHE 0.003 0.001 PHE C 19 TYR 0.005 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.258 Fit side-chains REVERT: A 34 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7476 (tt) REVERT: D 11 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7410 (mt-10) REVERT: B 15 GLN cc_start: 0.8659 (pm20) cc_final: 0.8169 (pm20) REVERT: J 35 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.5244 (tpt) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.0854 time to fit residues: 8.2844 Evaluate side-chains 82 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2370 Z= 0.267 Angle : 0.646 6.625 3180 Z= 0.344 Chirality : 0.056 0.135 360 Planarity : 0.002 0.012 400 Dihedral : 5.630 17.046 310 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.83 % Allowed : 16.67 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.39), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.30), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 13 PHE 0.003 0.001 PHE C 19 TYR 0.006 0.001 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.270 Fit side-chains REVERT: A 34 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7447 (tt) REVERT: B 15 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: J 35 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.5207 (tpt) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.0849 time to fit residues: 8.4023 Evaluate side-chains 85 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2370 Z= 0.255 Angle : 0.645 6.624 3180 Z= 0.343 Chirality : 0.056 0.134 360 Planarity : 0.002 0.012 400 Dihedral : 5.599 16.899 310 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.42 % Allowed : 17.08 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.39), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.30), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 13 PHE 0.003 0.001 PHE C 19 TYR 0.007 0.001 TYR E 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.259 Fit side-chains REVERT: A 34 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7457 (tt) REVERT: D 11 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7341 (mt-10) REVERT: B 15 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: J 35 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.5201 (tpt) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.0900 time to fit residues: 8.6186 Evaluate side-chains 85 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2370 Z= 0.185 Angle : 0.617 6.982 3180 Z= 0.325 Chirality : 0.056 0.132 360 Planarity : 0.002 0.010 400 Dihedral : 5.463 17.623 310 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.00 % Allowed : 17.50 % Favored : 77.50 % 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: -2.79 (0.40), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 13 PHE 0.003 0.001 PHE H 19 TYR 0.006 0.001 TYR G 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.288 Fit side-chains REVERT: A 34 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7552 (tt) REVERT: B 15 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.5892 (tp-100) REVERT: J 10 TYR cc_start: 0.7508 (m-80) cc_final: 0.5313 (p90) REVERT: J 35 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.5099 (tpt) outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 0.0890 time to fit residues: 8.6155 Evaluate side-chains 84 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.172202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.154447 restraints weight = 3136.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.158726 restraints weight = 1524.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.161724 restraints weight = 913.574| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 2370 Z= 0.570 Angle : 0.802 6.087 3180 Z= 0.433 Chirality : 0.059 0.138 360 Planarity : 0.003 0.017 400 Dihedral : 6.081 17.095 310 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.42 % Allowed : 16.67 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.37), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.28), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 13 PHE 0.006 0.002 PHE J 20 TYR 0.017 0.003 TYR H 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 902.12 seconds wall clock time: 17 minutes 28.59 seconds (1048.59 seconds total)