Starting phenix.real_space_refine on Mon Sep 23 13:00:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/09_2024/8bfa_16018.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/09_2024/8bfa_16018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/09_2024/8bfa_16018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/09_2024/8bfa_16018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/09_2024/8bfa_16018.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/09_2024/8bfa_16018.cif" } resolution = 3.0 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= 0.002 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 1810 2.51 5 N 510 2.21 5 O 530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2860 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "B" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "D" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "E" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "F" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "G" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "H" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "J" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Time building chain proxies: 2.28, per 1000 atoms: 0.80 Number of scatterers: 2860 At special positions: 0 Unit cell: (90.47, 67.23, 39.84, 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 530 8.00 N 510 7.00 C 1810 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: 0.61 Conformation dependent library (CDL) restraints added in 391.9 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: 620 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 52.1% 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 3 through 7 removed outlier: 6.163A pdb=" N PHE E 4 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP G 7 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS E 6 " --> pdb=" O ASP G 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.385A pdb=" N GLU A 11 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N HIS C 14 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS A 13 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LYS C 16 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN A 15 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU E 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS G 14 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS E 13 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LYS G 16 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN E 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS I 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N HIS G 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS I 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN G 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.818A pdb=" N SER C 26 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN A 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER E 26 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN C 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER G 26 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN E 27 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER I 26 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN G 27 " --> pdb=" O SER I 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.398A pdb=" N ALA A 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY C 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ILE A 32 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET C 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LEU A 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA C 30 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLY E 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE C 32 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N MET E 35 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LEU C 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA E 30 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLY G 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N ILE E 32 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET G 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LEU E 34 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA G 30 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY I 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ILE G 32 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET I 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N LEU G 34 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 7 removed outlier: 6.150A pdb=" N PHE D 4 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASP F 7 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS D 6 " --> pdb=" O ASP F 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 16 removed outlier: 6.393A pdb=" N GLU B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS D 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N HIS B 13 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS D 16 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN B 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU D 11 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS F 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS D 13 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LYS F 16 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN D 15 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU F 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N HIS H 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS F 13 " --> pdb=" O HIS H 14 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LYS H 16 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN F 15 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU H 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS J 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS H 13 " --> pdb=" O HIS J 14 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LYS J 16 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN H 15 " --> pdb=" O LYS J 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.835A pdb=" N SER D 26 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN B 27 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER F 26 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN D 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER H 26 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN F 27 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER J 26 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN H 27 " --> pdb=" O SER J 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.406A pdb=" N ALA B 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLY D 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ILE B 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET D 35 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N LEU B 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA D 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY F 33 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ILE D 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N MET F 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LEU D 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA F 30 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLY H 33 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ILE F 32 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET H 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N LEU F 34 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA H 30 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY J 33 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N ILE H 32 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N MET J 35 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N LEU H 34 " --> pdb=" O MET J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 46 hydrogen bonds defined for protein. 138 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: 0.67 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 980 1.34 - 1.46: 648 1.46 - 1.57: 1272 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2920 Sorted by residual: bond pdb=" N ARG J 5 " pdb=" CA ARG J 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.65e+00 bond pdb=" N ARG B 5 " pdb=" CA ARG B 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.55e+00 bond pdb=" N ARG I 5 " pdb=" CA ARG I 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.54e+00 bond pdb=" N ARG E 5 " pdb=" CA ARG E 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.45e+00 bond pdb=" N ARG C 5 " pdb=" CA ARG C 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.43e+00 ... (remaining 2915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.54: 3433 0.54 - 1.08: 392 1.08 - 1.61: 45 1.61 - 2.15: 20 2.15 - 2.69: 10 Bond angle restraints: 3900 Sorted by residual: angle pdb=" CA ARG A 5 " pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 120.24 118.31 1.93 1.06e+00 8.90e-01 3.33e+00 angle pdb=" CA ARG B 5 " pdb=" C ARG B 5 " pdb=" O ARG B 5 " ideal model delta sigma weight residual 120.24 118.32 1.92 1.06e+00 8.90e-01 3.27e+00 angle pdb=" CA ARG G 5 " pdb=" C ARG G 5 " pdb=" O ARG G 5 " ideal model delta sigma weight residual 120.24 118.34 1.90 1.06e+00 8.90e-01 3.22e+00 angle pdb=" CA ARG F 5 " pdb=" C ARG F 5 " pdb=" O ARG F 5 " ideal model delta sigma weight residual 120.24 118.34 1.90 1.06e+00 8.90e-01 3.21e+00 angle pdb=" CA ARG I 5 " pdb=" C ARG I 5 " pdb=" O ARG I 5 " ideal model delta sigma weight residual 120.24 118.35 1.89 1.06e+00 8.90e-01 3.19e+00 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1440 13.04 - 26.08: 90 26.08 - 39.13: 40 39.13 - 52.17: 30 52.17 - 65.21: 10 Dihedral angle restraints: 1610 sinusoidal: 610 harmonic: 1000 Sorted by residual: dihedral pdb=" CA LEU E 34 " pdb=" CB LEU E 34 " pdb=" CG LEU E 34 " pdb=" CD1 LEU E 34 " ideal model delta sinusoidal sigma weight residual 180.00 139.97 40.03 3 1.50e+01 4.44e-03 7.12e+00 dihedral pdb=" CA LEU I 34 " pdb=" CB LEU I 34 " pdb=" CG LEU I 34 " pdb=" CD1 LEU I 34 " ideal model delta sinusoidal sigma weight residual 180.00 140.02 39.98 3 1.50e+01 4.44e-03 7.11e+00 dihedral pdb=" CA LEU H 34 " pdb=" CB LEU H 34 " pdb=" CG LEU H 34 " pdb=" CD1 LEU H 34 " ideal model delta sinusoidal sigma weight residual 180.00 140.03 39.97 3 1.50e+01 4.44e-03 7.10e+00 ... (remaining 1607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 149 0.024 - 0.049: 133 0.049 - 0.073: 48 0.073 - 0.098: 3 0.098 - 0.122: 57 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ARG H 5 " pdb=" N ARG H 5 " pdb=" C ARG H 5 " pdb=" CB ARG H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ARG E 5 " pdb=" N ARG E 5 " pdb=" C ARG E 5 " pdb=" CB ARG E 5 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ARG F 5 " pdb=" N ARG F 5 " pdb=" C ARG F 5 " pdb=" CB ARG F 5 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 387 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.003 2.00e-02 2.50e+03 2.70e-03 1.28e-01 pdb=" CG PHE A 4 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 4 " -0.002 2.00e-02 2.50e+03 2.51e-03 1.11e-01 pdb=" CG PHE G 4 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE G 4 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE G 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE G 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 4 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE G 4 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 4 " -0.002 2.00e-02 2.50e+03 2.50e-03 1.10e-01 pdb=" CG PHE C 4 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE C 4 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 4 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 4 " -0.000 2.00e-02 2.50e+03 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1663 3.05 - 3.51: 2612 3.51 - 3.98: 4531 3.98 - 4.44: 4981 4.44 - 4.90: 10405 Nonbonded interactions: 24192 Sorted by model distance: nonbonded pdb=" NZ LYS G 28 " pdb=" OE2 GLU H 11 " model vdw 2.592 3.120 nonbonded pdb=" NZ LYS E 28 " pdb=" OE2 GLU F 11 " model vdw 2.603 3.120 nonbonded pdb=" NZ LYS F 28 " pdb=" OE2 GLU G 11 " model vdw 2.609 3.120 nonbonded pdb=" NZ LYS I 28 " pdb=" OE2 GLU J 11 " model vdw 2.618 3.120 nonbonded pdb=" NZ LYS H 28 " pdb=" OE2 GLU I 11 " model vdw 2.618 3.120 ... (remaining 24187 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 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: 1.130 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: 0.020 Set scattering table: 0.030 Process input model: 11.660 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.002 0.028 2920 Z= 0.171 Angle : 0.386 2.691 3900 Z= 0.246 Chirality : 0.052 0.122 390 Planarity : 0.001 0.003 520 Dihedral : 13.944 65.212 990 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: -3.13 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 6 PHE 0.006 0.001 PHE A 4 TYR 0.004 0.001 TYR C 10 ARG 0.001 0.000 ARG E 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 50 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.322 Fit side-chains REVERT: G 28 LYS cc_start: 0.8369 (mttt) cc_final: 0.8006 (mttt) REVERT: H 28 LYS cc_start: 0.8370 (mttt) cc_final: 0.8099 (mttt) REVERT: I 35 MET cc_start: 0.8337 (mtt) cc_final: 0.8137 (mtm) REVERT: J 23 ASP cc_start: 0.7789 (m-30) cc_final: 0.7255 (p0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 1.3154 time to fit residues: 67.4111 Evaluate side-chains 32 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 13 HIS B 27 ASN C 27 ASN D 27 ASN E 13 HIS E 27 ASN F 27 ASN G 27 ASN H 27 ASN I 27 ASN J 27 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 2920 Z= 0.648 Angle : 0.625 4.908 3900 Z= 0.342 Chirality : 0.054 0.139 390 Planarity : 0.004 0.027 520 Dihedral : 5.477 15.430 390 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 8.57 % Allowed : 8.21 % Favored : 83.21 % 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: -2.77 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 13 PHE 0.017 0.003 PHE F 4 TYR 0.013 0.003 TYR C 10 ARG 0.002 0.001 ARG D 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 65 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 41 time to evaluate : 0.321 Fit side-chains REVERT: A 1 ASP cc_start: 0.6876 (m-30) cc_final: 0.6582 (t0) REVERT: B 1 ASP cc_start: 0.6889 (m-30) cc_final: 0.6394 (t0) REVERT: B 28 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8474 (mtpt) REVERT: C 1 ASP cc_start: 0.6591 (m-30) cc_final: 0.6030 (OUTLIER) REVERT: C 5 ARG cc_start: 0.6736 (mtp180) cc_final: 0.6413 (tmt90) REVERT: C 28 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8202 (mtpt) REVERT: D 1 ASP cc_start: 0.6556 (m-30) cc_final: 0.5935 (t0) REVERT: E 1 ASP cc_start: 0.6837 (m-30) cc_final: 0.6084 (t0) REVERT: F 1 ASP cc_start: 0.6689 (m-30) cc_final: 0.6009 (t0) REVERT: F 5 ARG cc_start: 0.6888 (mtp180) cc_final: 0.6587 (ttt90) REVERT: G 1 ASP cc_start: 0.6913 (m-30) cc_final: 0.6253 (t0) REVERT: H 1 ASP cc_start: 0.6745 (m-30) cc_final: 0.5996 (t0) REVERT: I 1 ASP cc_start: 0.7086 (m-30) cc_final: 0.6307 (t0) REVERT: J 1 ASP cc_start: 0.6922 (m-30) cc_final: 0.6042 (t0) outliers start: 24 outliers final: 10 residues processed: 63 average time/residue: 1.2940 time to fit residues: 83.4041 Evaluate side-chains 45 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2920 Z= 0.315 Angle : 0.443 3.554 3900 Z= 0.248 Chirality : 0.052 0.133 390 Planarity : 0.002 0.009 520 Dihedral : 4.693 12.253 390 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.00 % Allowed : 13.21 % Favored : 81.79 % 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: -2.67 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 13 PHE 0.011 0.002 PHE D 4 TYR 0.007 0.002 TYR H 10 ARG 0.001 0.000 ARG G 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 65 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.308 Fit side-chains REVERT: A 5 ARG cc_start: 0.7457 (mtp180) cc_final: 0.7212 (tmt90) REVERT: B 1 ASP cc_start: 0.6733 (m-30) cc_final: 0.6307 (t0) REVERT: B 5 ARG cc_start: 0.7497 (mtp180) cc_final: 0.7192 (tmt90) REVERT: B 35 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7775 (ttp) REVERT: C 1 ASP cc_start: 0.6492 (m-30) cc_final: 0.5808 (t0) REVERT: C 5 ARG cc_start: 0.6711 (mtp180) cc_final: 0.6361 (tmt90) REVERT: D 1 ASP cc_start: 0.6556 (m-30) cc_final: 0.5905 (t0) REVERT: D 11 GLU cc_start: 0.7883 (tt0) cc_final: 0.7390 (tt0) REVERT: E 1 ASP cc_start: 0.6725 (m-30) cc_final: 0.6083 (t0) REVERT: F 1 ASP cc_start: 0.6610 (m-30) cc_final: 0.6060 (t0) REVERT: F 3 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6941 (tt0) REVERT: G 1 ASP cc_start: 0.6638 (m-30) cc_final: 0.5979 (t0) REVERT: H 1 ASP cc_start: 0.6535 (m-30) cc_final: 0.5995 (t0) REVERT: I 1 ASP cc_start: 0.7044 (m-30) cc_final: 0.6304 (t0) REVERT: J 1 ASP cc_start: 0.6910 (m-30) cc_final: 0.6096 (t0) outliers start: 14 outliers final: 7 residues processed: 61 average time/residue: 1.3462 time to fit residues: 83.9511 Evaluate side-chains 51 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J 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: 10.0000 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2920 Z= 0.237 Angle : 0.408 3.206 3900 Z= 0.227 Chirality : 0.051 0.131 390 Planarity : 0.001 0.005 520 Dihedral : 4.433 12.559 390 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % 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: -2.60 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.009 0.001 PHE D 4 TYR 0.004 0.001 TYR B 10 ARG 0.002 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 51 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.304 Fit side-chains REVERT: B 5 ARG cc_start: 0.7493 (mtp180) cc_final: 0.7180 (tmt90) REVERT: B 35 MET cc_start: 0.8130 (mtt) cc_final: 0.7828 (ttp) REVERT: C 5 ARG cc_start: 0.6691 (mtp180) cc_final: 0.6335 (tmt90) REVERT: D 11 GLU cc_start: 0.7924 (tt0) cc_final: 0.7342 (tt0) REVERT: F 1 ASP cc_start: 0.6651 (m-30) cc_final: 0.6305 (t0) REVERT: F 3 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6737 (tm-30) REVERT: F 5 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6532 (tmt90) REVERT: G 3 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6831 (tm-30) REVERT: H 1 ASP cc_start: 0.6682 (m-30) cc_final: 0.6115 (t0) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 1.5963 time to fit residues: 81.4811 Evaluate side-chains 44 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J 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: 20.0000 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2920 Z= 0.329 Angle : 0.462 3.845 3900 Z= 0.250 Chirality : 0.052 0.131 390 Planarity : 0.002 0.005 520 Dihedral : 4.733 12.314 390 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.00 % Allowed : 15.71 % Favored : 79.29 % 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: -2.54 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 13 PHE 0.010 0.002 PHE H 4 TYR 0.007 0.002 TYR I 10 ARG 0.001 0.000 ARG G 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 61 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.315 Fit side-chains REVERT: A 3 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7515 (tm-30) REVERT: B 3 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7370 (tm-30) REVERT: C 5 ARG cc_start: 0.6653 (mtp180) cc_final: 0.6307 (tmt90) REVERT: D 11 GLU cc_start: 0.7905 (tt0) cc_final: 0.7376 (tt0) REVERT: E 35 MET cc_start: 0.7762 (ttm) cc_final: 0.7554 (mtt) REVERT: F 3 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6797 (tm-30) REVERT: F 5 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6415 (tmt90) REVERT: F 11 GLU cc_start: 0.7914 (tt0) cc_final: 0.7680 (tt0) REVERT: G 3 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6772 (tm-30) REVERT: G 28 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8376 (mttt) outliers start: 14 outliers final: 5 residues processed: 57 average time/residue: 1.5012 time to fit residues: 87.3791 Evaluate side-chains 52 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J 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: 5.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2920 Z= 0.405 Angle : 0.514 5.382 3900 Z= 0.274 Chirality : 0.053 0.138 390 Planarity : 0.002 0.005 520 Dihedral : 5.072 13.386 390 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.29 % Allowed : 18.21 % 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: -2.46 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 14 PHE 0.011 0.002 PHE H 4 TYR 0.006 0.002 TYR C 10 ARG 0.001 0.001 ARG E 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 58 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.309 Fit side-chains REVERT: A 3 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7501 (tm-30) REVERT: B 3 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7396 (tm-30) REVERT: F 3 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6873 (tm-30) REVERT: F 5 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6405 (tmt90) REVERT: G 3 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6906 (tm-30) REVERT: G 28 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8455 (mttt) REVERT: H 28 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8388 (mttt) REVERT: H 32 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7946 (mt) REVERT: J 1 ASP cc_start: 0.7097 (m-30) cc_final: 0.6809 (m-30) outliers start: 12 outliers final: 4 residues processed: 55 average time/residue: 1.4545 time to fit residues: 81.7635 Evaluate side-chains 52 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J 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: 2.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.0770 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 HIS J 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2920 Z= 0.150 Angle : 0.390 3.631 3900 Z= 0.216 Chirality : 0.051 0.132 390 Planarity : 0.001 0.006 520 Dihedral : 4.306 12.497 390 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.07 % Allowed : 22.50 % Favored : 76.43 % 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: -2.40 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 13 PHE 0.006 0.001 PHE H 4 TYR 0.009 0.001 TYR I 10 ARG 0.001 0.000 ARG G 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 53 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.340 Fit side-chains REVERT: A 3 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7506 (tm-30) REVERT: B 3 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7190 (tm-30) REVERT: B 28 LYS cc_start: 0.8764 (mttm) cc_final: 0.7166 (mmpt) REVERT: C 5 ARG cc_start: 0.6755 (mtp180) cc_final: 0.6314 (tmt90) REVERT: D 11 GLU cc_start: 0.7885 (tt0) cc_final: 0.7653 (tt0) REVERT: D 26 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.8861 (p) REVERT: E 11 GLU cc_start: 0.7985 (tt0) cc_final: 0.7635 (tt0) REVERT: F 3 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6830 (tm-30) REVERT: G 3 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6812 (tm-30) REVERT: G 28 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8350 (mtmt) REVERT: H 28 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8429 (mttt) REVERT: J 26 SER cc_start: 0.9045 (p) cc_final: 0.8559 (p) outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 1.5117 time to fit residues: 81.8606 Evaluate side-chains 49 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E 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: 10.0000 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2920 Z= 0.297 Angle : 0.458 4.518 3900 Z= 0.244 Chirality : 0.052 0.132 390 Planarity : 0.002 0.007 520 Dihedral : 4.735 13.176 390 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.43 % Allowed : 20.71 % Favored : 77.86 % 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: -2.37 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.011 0.002 PHE J 4 TYR 0.008 0.002 TYR J 10 ARG 0.001 0.000 ARG B 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 46 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.315 Fit side-chains REVERT: A 3 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7475 (tm-30) REVERT: B 3 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7269 (tm-30) REVERT: B 28 LYS cc_start: 0.8833 (mttm) cc_final: 0.8582 (mttt) REVERT: D 11 GLU cc_start: 0.7853 (tt0) cc_final: 0.7504 (tt0) REVERT: E 11 GLU cc_start: 0.7962 (tt0) cc_final: 0.7745 (tt0) REVERT: F 3 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6857 (tm-30) REVERT: F 5 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6488 (tmt90) REVERT: G 3 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6833 (tm-30) REVERT: G 28 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8390 (mttt) REVERT: H 28 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8474 (mttt) REVERT: J 26 SER cc_start: 0.9031 (p) cc_final: 0.8557 (p) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 1.3373 time to fit residues: 61.6663 Evaluate side-chains 43 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.0270 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2920 Z= 0.134 Angle : 0.376 3.669 3900 Z= 0.208 Chirality : 0.051 0.135 390 Planarity : 0.001 0.007 520 Dihedral : 4.128 12.054 390 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.71 % Allowed : 21.43 % Favored : 77.86 % 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: -2.40 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.006 0.001 PHE H 4 TYR 0.010 0.001 TYR J 10 ARG 0.001 0.000 ARG B 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 48 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.279 Fit side-chains REVERT: A 3 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7466 (tm-30) REVERT: B 3 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7194 (tm-30) REVERT: C 5 ARG cc_start: 0.6719 (mtp180) cc_final: 0.6261 (tmt90) REVERT: F 3 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6846 (tm-30) REVERT: G 3 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6912 (tm-30) REVERT: G 28 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8409 (mttt) REVERT: H 28 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8562 (mttt) REVERT: J 26 SER cc_start: 0.9001 (p) cc_final: 0.8485 (p) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 1.5016 time to fit residues: 73.6437 Evaluate side-chains 45 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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: 4.9990 chunk 21 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 2920 Z= 0.463 Angle : 0.545 5.222 3900 Z= 0.288 Chirality : 0.053 0.132 390 Planarity : 0.002 0.007 520 Dihedral : 5.157 14.424 390 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.86 % Allowed : 19.29 % Favored : 77.86 % 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: -2.34 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 13 PHE 0.014 0.002 PHE J 4 TYR 0.006 0.002 TYR A 10 ARG 0.002 0.001 ARG H 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 50 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.284 Fit side-chains REVERT: A 3 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7451 (tm-30) REVERT: B 3 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7311 (tm-30) REVERT: D 11 GLU cc_start: 0.7820 (tt0) cc_final: 0.7488 (tt0) REVERT: F 3 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6781 (tm-30) REVERT: F 5 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6465 (tmt90) REVERT: G 3 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6917 (tm-30) REVERT: H 28 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8383 (mttt) REVERT: H 32 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7948 (mt) REVERT: J 26 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8561 (p) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 1.2908 time to fit residues: 63.5277 Evaluate side-chains 48 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J 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: 10.0000 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.130989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.113142 restraints weight = 3589.929| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.64 r_work: 0.3878 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2920 Z= 0.165 Angle : 0.400 3.665 3900 Z= 0.220 Chirality : 0.051 0.133 390 Planarity : 0.001 0.008 520 Dihedral : 4.407 13.382 390 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.79 % Allowed : 22.14 % Favored : 76.07 % 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: -2.40 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 13 PHE 0.007 0.001 PHE H 4 TYR 0.010 0.001 TYR I 10 ARG 0.001 0.000 ARG B 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.20 seconds wall clock time: 30 minutes 44.98 seconds (1844.98 seconds total)