Starting phenix.real_space_refine on Fri Apr 5 13:30:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/04_2024/8owe_17235.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/04_2024/8owe_17235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/04_2024/8owe_17235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/04_2024/8owe_17235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/04_2024/8owe_17235.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/04_2024/8owe_17235.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 1880 2.51 5 N 515 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2940 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 283 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "B" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 283 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "C" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 283 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 283 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 283 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "F" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "G" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "H" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "I" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "J" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Time building chain proxies: 1.98, per 1000 atoms: 0.67 Number of scatterers: 2940 At special positions: 0 Unit cell: (79.8, 106.05, 50.4, 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 535 8.00 N 515 7.00 C 1880 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 603.4 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.116A pdb=" N TYR A 10 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR B 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR C 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR D 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 23 Processing sheet with id=AA3, first strand: chain 'F' and resid 2 through 23 removed outlier: 8.867A pdb=" N ALA F 2 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N ARG G 5 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE F 4 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ASP G 7 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N HIS F 6 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N GLY G 9 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER F 8 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU G 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR F 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS G 13 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL F 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN G 15 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N HIS F 14 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N LEU G 17 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LYS F 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N PHE G 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL F 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N ALA G 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N PHE F 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ASP G 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU F 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ALA G 2 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N ARG H 5 " --> pdb=" O ALA G 2 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE G 4 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ASP H 7 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N HIS G 6 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N GLY H 9 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER G 8 " --> pdb=" O GLY H 9 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU H 11 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR G 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS H 13 " --> pdb=" O TYR G 10 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL G 12 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN H 15 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N HIS G 14 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N LEU H 17 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LYS G 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N PHE H 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL G 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N ALA H 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N PHE G 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ASP H 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU G 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ALA H 2 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N ARG I 5 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE H 4 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N ASP I 7 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N HIS H 6 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N GLY I 9 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER H 8 " --> pdb=" O GLY I 9 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU I 11 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR H 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS I 13 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL H 12 " --> pdb=" O HIS I 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN I 15 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N HIS H 14 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N LEU I 17 " --> pdb=" O HIS H 14 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LYS H 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N PHE I 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL H 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N ALA I 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N PHE H 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ASP I 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU H 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ALA I 2 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N ARG J 5 " --> pdb=" O ALA I 2 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE I 4 " --> pdb=" O ARG J 5 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N ASP J 7 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N HIS I 6 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N GLY J 9 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER I 8 " --> pdb=" O GLY J 9 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU J 11 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR I 10 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS J 13 " --> pdb=" O TYR I 10 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL I 12 " --> pdb=" O HIS J 13 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN J 15 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N HIS I 14 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 10.081A pdb=" N LEU J 17 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LYS I 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N PHE J 19 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL I 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ALA J 21 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N PHE I 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ASP J 23 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU I 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 29 through 36 removed outlier: 6.784A pdb=" N ALA G 30 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE F 31 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE G 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY F 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA H 30 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE G 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE H 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY G 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA I 30 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE H 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE I 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY H 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA J 30 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE I 31 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE J 32 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY I 33 " --> pdb=" O ILE J 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: 0.59 Time building geometry restraints manager: 1.13 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: 819 1.33 - 1.45: 560 1.45 - 1.57: 1587 1.57 - 1.69: 14 1.69 - 1.81: 20 Bond restraints: 3000 Sorted by residual: bond pdb=" CA MET J 35 " pdb=" C MET J 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.37e+01 bond pdb=" CA MET H 35 " pdb=" C MET H 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" CA MET F 35 " pdb=" C MET F 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" CA MET I 35 " pdb=" C MET I 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" CA MET G 35 " pdb=" C MET G 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.35e+01 ... (remaining 2995 not shown) Histogram of bond angle deviations from ideal: 100.17 - 105.71: 73 105.71 - 111.26: 918 111.26 - 116.80: 854 116.80 - 122.35: 1653 122.35 - 127.89: 522 Bond angle restraints: 4020 Sorted by residual: angle pdb=" O ILE E 32 " pdb=" C ILE E 32 " pdb=" N GLY E 33 " ideal model delta sigma weight residual 122.76 114.63 8.13 1.04e+00 9.25e-01 6.11e+01 angle pdb=" O ILE D 32 " pdb=" C ILE D 32 " pdb=" N GLY D 33 " ideal model delta sigma weight residual 122.76 114.64 8.12 1.04e+00 9.25e-01 6.09e+01 angle pdb=" O ILE C 32 " pdb=" C ILE C 32 " pdb=" N GLY C 33 " ideal model delta sigma weight residual 122.76 114.66 8.10 1.04e+00 9.25e-01 6.07e+01 angle pdb=" O ILE A 32 " pdb=" C ILE A 32 " pdb=" N GLY A 33 " ideal model delta sigma weight residual 122.76 114.66 8.10 1.04e+00 9.25e-01 6.07e+01 angle pdb=" O ILE B 32 " pdb=" C ILE B 32 " pdb=" N GLY B 33 " ideal model delta sigma weight residual 122.76 114.68 8.08 1.04e+00 9.25e-01 6.03e+01 ... (remaining 4015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1395 17.40 - 34.79: 170 34.79 - 52.19: 60 52.19 - 69.58: 20 69.58 - 86.98: 25 Dihedral angle restraints: 1670 sinusoidal: 635 harmonic: 1035 Sorted by residual: dihedral pdb=" C VAL B 24 " pdb=" N VAL B 24 " pdb=" CA VAL B 24 " pdb=" CB VAL B 24 " ideal model delta harmonic sigma weight residual -122.00 -136.33 14.33 0 2.50e+00 1.60e-01 3.28e+01 dihedral pdb=" C VAL E 24 " pdb=" N VAL E 24 " pdb=" CA VAL E 24 " pdb=" CB VAL E 24 " ideal model delta harmonic sigma weight residual -122.00 -136.33 14.33 0 2.50e+00 1.60e-01 3.28e+01 dihedral pdb=" C VAL C 24 " pdb=" N VAL C 24 " pdb=" CA VAL C 24 " pdb=" CB VAL C 24 " ideal model delta harmonic sigma weight residual -122.00 -136.32 14.32 0 2.50e+00 1.60e-01 3.28e+01 ... (remaining 1667 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.096: 169 0.096 - 0.189: 175 0.189 - 0.281: 41 0.281 - 0.373: 20 0.373 - 0.465: 20 Chirality restraints: 425 Sorted by residual: chirality pdb=" CA VAL D 24 " pdb=" N VAL D 24 " pdb=" C VAL D 24 " pdb=" CB VAL D 24 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA VAL A 24 " pdb=" N VAL A 24 " pdb=" C VAL A 24 " pdb=" CB VAL A 24 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA VAL B 24 " pdb=" N VAL B 24 " pdb=" C VAL B 24 " pdb=" CB VAL B 24 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.40e+00 ... (remaining 422 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 13 " 0.117 2.00e-02 2.50e+03 8.75e-02 1.15e+02 pdb=" CG HIS I 13 " -0.122 2.00e-02 2.50e+03 pdb=" ND1 HIS I 13 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 HIS I 13 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS I 13 " 0.072 2.00e-02 2.50e+03 pdb=" NE2 HIS I 13 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS J 13 " 0.117 2.00e-02 2.50e+03 8.75e-02 1.15e+02 pdb=" CG HIS J 13 " -0.122 2.00e-02 2.50e+03 pdb=" ND1 HIS J 13 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 HIS J 13 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS J 13 " 0.072 2.00e-02 2.50e+03 pdb=" NE2 HIS J 13 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 13 " 0.117 2.00e-02 2.50e+03 8.75e-02 1.15e+02 pdb=" CG HIS F 13 " -0.122 2.00e-02 2.50e+03 pdb=" ND1 HIS F 13 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 HIS F 13 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS F 13 " 0.072 2.00e-02 2.50e+03 pdb=" NE2 HIS F 13 " 0.062 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 7 2.44 - 3.06: 1812 3.06 - 3.67: 4609 3.67 - 4.29: 6852 4.29 - 4.90: 12265 Nonbonded interactions: 25545 Sorted by model distance: nonbonded pdb=" OD2 ASP B 7 " pdb=" NE ARG C 5 " model vdw 1.831 2.520 nonbonded pdb=" OD2 ASP C 7 " pdb=" NE ARG D 5 " model vdw 1.831 2.520 nonbonded pdb=" OD2 ASP A 7 " pdb=" NE ARG B 5 " model vdw 1.831 2.520 nonbonded pdb=" OD2 ASP D 7 " pdb=" NE ARG E 5 " model vdw 1.831 2.520 nonbonded pdb=" NE2 HIS A 14 " pdb=" OD2 ASP H 1 " model vdw 2.399 2.520 ... (remaining 25540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 4 through 40) selection = (chain 'G' and resid 4 through 40) selection = (chain 'H' and resid 4 through 40) selection = (chain 'I' and resid 4 through 40) selection = (chain 'J' and resid 4 through 40) } 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: 0.660 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: 3.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.750 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.014 0.056 3000 Z= 0.956 Angle : 2.465 9.004 4020 Z= 1.707 Chirality : 0.170 0.465 425 Planarity : 0.028 0.144 525 Dihedral : 22.521 86.977 1020 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 18.33 % Allowed : 13.33 % Favored : 68.33 % Cbeta Deviations : 6.15 % 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 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.023 0.010 HIS J 14 PHE 0.060 0.012 PHE J 19 TYR 0.024 0.010 TYR E 10 ARG 0.006 0.002 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 163 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7465 (tppt) REVERT: A 35 MET cc_start: 0.7941 (ptt) cc_final: 0.6000 (mmp) REVERT: E 31 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.7888 (tp) REVERT: F 28 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6723 (mmtm) REVERT: G 8 SER cc_start: 0.8545 (p) cc_final: 0.8150 (p) REVERT: H 39 VAL cc_start: 0.9128 (t) cc_final: 0.8743 (m) REVERT: H 40 VAL cc_start: 0.8571 (t) cc_final: 0.8361 (t) REVERT: J 16 LYS cc_start: 0.7706 (ttmt) cc_final: 0.7249 (mmmt) outliers start: 55 outliers final: 9 residues processed: 180 average time/residue: 0.1511 time to fit residues: 31.7039 Evaluate side-chains 106 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 HIS F 6 HIS F 27 ASN G 6 HIS G 27 ASN H 6 HIS H 27 ASN I 6 HIS J 6 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3000 Z= 0.304 Angle : 0.710 6.341 4020 Z= 0.395 Chirality : 0.050 0.159 425 Planarity : 0.004 0.018 525 Dihedral : 11.311 59.901 431 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 9.67 % Allowed : 20.33 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 13 PHE 0.019 0.002 PHE G 4 TYR 0.009 0.001 TYR E 10 ARG 0.003 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.330 Fit side-chains REVERT: A 28 LYS cc_start: 0.8766 (ptpt) cc_final: 0.7395 (tppt) REVERT: A 35 MET cc_start: 0.7330 (ptt) cc_final: 0.5274 (mmp) REVERT: B 12 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7646 (m) REVERT: B 22 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7700 (tp30) REVERT: C 22 GLU cc_start: 0.8168 (tm-30) cc_final: 0.6558 (tm-30) REVERT: F 10 TYR cc_start: 0.7990 (t80) cc_final: 0.7556 (t80) REVERT: F 28 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6326 (mmtm) REVERT: G 23 ASP cc_start: 0.7217 (t0) cc_final: 0.6868 (t0) REVERT: G 35 MET cc_start: 0.8225 (ttm) cc_final: 0.7978 (ttt) REVERT: H 23 ASP cc_start: 0.7389 (t0) cc_final: 0.6769 (t0) REVERT: J 13 HIS cc_start: 0.6757 (OUTLIER) cc_final: 0.6241 (t70) REVERT: J 23 ASP cc_start: 0.6019 (t0) cc_final: 0.5807 (t0) outliers start: 29 outliers final: 18 residues processed: 131 average time/residue: 0.1396 time to fit residues: 21.9107 Evaluate side-chains 113 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN G 27 ASN H 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3000 Z= 0.458 Angle : 0.739 6.067 4020 Z= 0.414 Chirality : 0.049 0.151 425 Planarity : 0.004 0.027 525 Dihedral : 10.239 49.775 425 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 9.33 % Allowed : 26.33 % Favored : 64.33 % 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: -3.52 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 13 PHE 0.016 0.003 PHE J 4 TYR 0.017 0.003 TYR E 10 ARG 0.003 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.350 Fit side-chains REVERT: A 28 LYS cc_start: 0.8534 (ptpt) cc_final: 0.7010 (tppt) REVERT: A 35 MET cc_start: 0.7503 (ptt) cc_final: 0.5171 (mmp) REVERT: B 22 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7956 (tm-30) REVERT: C 22 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8007 (tm-30) REVERT: F 28 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.5786 (mtpp) REVERT: I 23 ASP cc_start: 0.7687 (t0) cc_final: 0.7201 (t0) outliers start: 28 outliers final: 22 residues processed: 108 average time/residue: 0.1504 time to fit residues: 19.2510 Evaluate side-chains 105 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN H 27 ASN I 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 3000 Z= 0.470 Angle : 0.716 5.796 4020 Z= 0.398 Chirality : 0.049 0.139 425 Planarity : 0.004 0.020 525 Dihedral : 9.696 45.018 423 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 8.67 % Allowed : 29.00 % Favored : 62.33 % 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: -3.66 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS B 13 PHE 0.019 0.003 PHE J 19 TYR 0.012 0.002 TYR E 10 ARG 0.003 0.001 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.355 Fit side-chains REVERT: B 11 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 22 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7578 (tm-30) REVERT: C 28 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8705 (ptpp) REVERT: D 13 HIS cc_start: 0.7620 (t-90) cc_final: 0.6799 (m-70) REVERT: D 22 GLU cc_start: 0.8670 (tm-30) cc_final: 0.7214 (tm-30) REVERT: F 28 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.5517 (mtpp) REVERT: I 10 TYR cc_start: 0.8748 (t80) cc_final: 0.8443 (t80) outliers start: 26 outliers final: 20 residues processed: 102 average time/residue: 0.1440 time to fit residues: 17.5367 Evaluate side-chains 101 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.0040 overall best weight: 3.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3000 Z= 0.251 Angle : 0.610 5.815 4020 Z= 0.326 Chirality : 0.049 0.142 425 Planarity : 0.003 0.012 525 Dihedral : 9.177 45.771 423 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 8.33 % Allowed : 29.33 % Favored : 62.33 % 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: -3.67 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 13 PHE 0.008 0.002 PHE E 19 TYR 0.006 0.001 TYR J 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 0.345 Fit side-chains REVERT: B 22 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 13 HIS cc_start: 0.7495 (t-90) cc_final: 0.6934 (m-70) REVERT: C 28 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8728 (ptpp) REVERT: D 13 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6690 (m-70) REVERT: D 22 GLU cc_start: 0.8600 (tm-30) cc_final: 0.7134 (tm-30) REVERT: F 28 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.5296 (mtpp) REVERT: H 5 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7473 (ttt180) outliers start: 25 outliers final: 18 residues processed: 98 average time/residue: 0.1513 time to fit residues: 17.8057 Evaluate side-chains 101 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 30.0000 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7608 moved from start: 0.7339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3000 Z= 0.361 Angle : 0.642 5.211 4020 Z= 0.347 Chirality : 0.048 0.136 425 Planarity : 0.003 0.017 525 Dihedral : 9.253 44.698 423 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 9.33 % Allowed : 28.33 % Favored : 62.33 % 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: -3.63 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 14 PHE 0.014 0.002 PHE J 19 TYR 0.009 0.002 TYR E 10 ARG 0.002 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 0.346 Fit side-chains REVERT: B 22 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 13 HIS cc_start: 0.7547 (t-90) cc_final: 0.7030 (m-70) REVERT: D 13 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.6755 (m-70) REVERT: D 22 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7193 (tm-30) REVERT: F 28 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.5179 (mtpp) REVERT: H 5 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7612 (ttt180) REVERT: I 13 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7436 (t-170) REVERT: I 28 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8058 (pttp) outliers start: 28 outliers final: 21 residues processed: 96 average time/residue: 0.1596 time to fit residues: 18.0469 Evaluate side-chains 103 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN I 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3000 Z= 0.330 Angle : 0.641 5.843 4020 Z= 0.341 Chirality : 0.049 0.136 425 Planarity : 0.003 0.016 525 Dihedral : 9.117 44.209 423 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 10.33 % Allowed : 26.67 % Favored : 63.00 % 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: -3.65 (0.32), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS B 13 PHE 0.012 0.002 PHE D 20 TYR 0.011 0.002 TYR C 10 ARG 0.002 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 0.359 Fit side-chains REVERT: B 11 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7556 (tm-30) REVERT: B 22 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7442 (tm-30) REVERT: C 13 HIS cc_start: 0.7516 (t-90) cc_final: 0.6963 (m-70) REVERT: D 11 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: D 13 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.6923 (m-70) REVERT: D 22 GLU cc_start: 0.8602 (tm-30) cc_final: 0.7144 (tm-30) REVERT: F 11 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7278 (tm-30) REVERT: F 28 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.5122 (tppp) REVERT: H 5 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7669 (ttt180) outliers start: 31 outliers final: 23 residues processed: 102 average time/residue: 0.1440 time to fit residues: 17.5332 Evaluate side-chains 106 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 79 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 18 optimal weight: 0.0470 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.7627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3000 Z= 0.232 Angle : 0.600 6.425 4020 Z= 0.319 Chirality : 0.049 0.142 425 Planarity : 0.003 0.017 525 Dihedral : 8.572 46.644 421 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 8.67 % Allowed : 29.67 % Favored : 61.67 % 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: -3.63 (0.32), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 13 PHE 0.008 0.001 PHE J 19 TYR 0.018 0.002 TYR I 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 0.344 Fit side-chains REVERT: B 11 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7543 (tm-30) REVERT: B 22 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7408 (tm-30) REVERT: C 13 HIS cc_start: 0.7473 (t-90) cc_final: 0.6987 (m-70) REVERT: D 11 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: D 13 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6910 (m-70) REVERT: D 22 GLU cc_start: 0.8598 (tm-30) cc_final: 0.7125 (tm-30) REVERT: F 28 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.5007 (tppp) REVERT: H 5 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7645 (ttt180) outliers start: 26 outliers final: 19 residues processed: 98 average time/residue: 0.1439 time to fit residues: 16.7968 Evaluate side-chains 102 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN G 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.7749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3000 Z= 0.217 Angle : 0.601 6.411 4020 Z= 0.316 Chirality : 0.049 0.141 425 Planarity : 0.002 0.015 525 Dihedral : 8.429 46.604 421 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 7.67 % Allowed : 29.67 % Favored : 62.67 % 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: -3.62 (0.32), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 13 PHE 0.010 0.001 PHE D 20 TYR 0.017 0.001 TYR I 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.344 Fit side-chains REVERT: B 11 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 22 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7436 (tm-30) REVERT: C 13 HIS cc_start: 0.7447 (t-90) cc_final: 0.6969 (m-70) REVERT: D 11 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: D 13 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.6906 (m-70) REVERT: D 22 GLU cc_start: 0.8558 (tm-30) cc_final: 0.7124 (tm-30) REVERT: F 28 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.5022 (tppp) REVERT: J 11 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7240 (tm-30) outliers start: 23 outliers final: 18 residues processed: 94 average time/residue: 0.1373 time to fit residues: 15.4786 Evaluate side-chains 103 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.7803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3000 Z= 0.261 Angle : 0.644 7.043 4020 Z= 0.336 Chirality : 0.049 0.138 425 Planarity : 0.003 0.015 525 Dihedral : 8.441 45.372 421 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 6.67 % Allowed : 30.67 % Favored : 62.67 % 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: -3.67 (0.32), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.25), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 13 PHE 0.009 0.002 PHE J 19 TYR 0.017 0.002 TYR I 10 ARG 0.001 0.000 ARG A 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.349 Fit side-chains REVERT: B 11 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 22 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7440 (tm-30) REVERT: C 13 HIS cc_start: 0.7472 (t-90) cc_final: 0.6997 (m-70) REVERT: D 11 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: D 13 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.6914 (m-70) REVERT: D 22 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7145 (tm-30) REVERT: F 11 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7241 (tm-30) REVERT: F 28 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.5086 (tppp) REVERT: J 11 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7240 (tm-30) outliers start: 20 outliers final: 17 residues processed: 93 average time/residue: 0.1421 time to fit residues: 15.8305 Evaluate side-chains 103 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.108146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.094120 restraints weight = 6121.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.096211 restraints weight = 2650.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.097407 restraints weight = 1652.097| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3000 Z= 0.209 Angle : 0.625 6.752 4020 Z= 0.322 Chirality : 0.049 0.142 425 Planarity : 0.002 0.015 525 Dihedral : 8.268 47.587 421 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 6.33 % Allowed : 31.33 % Favored : 62.33 % 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: -3.69 (0.32), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.25), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 13 PHE 0.010 0.001 PHE D 20 TYR 0.014 0.001 TYR I 10 ARG 0.001 0.000 ARG E 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1053.42 seconds wall clock time: 19 minutes 31.53 seconds (1171.53 seconds total)