Starting phenix.real_space_refine on Tue Feb 13 07:30:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az5_15754/02_2024/8az5_15754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az5_15754/02_2024/8az5_15754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az5_15754/02_2024/8az5_15754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az5_15754/02_2024/8az5_15754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az5_15754/02_2024/8az5_15754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az5_15754/02_2024/8az5_15754_updated.pdb" } resolution = 2.3 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= 0.003 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: 3 Type Number sf(0) Gaussians C 2500 2.51 5 N 760 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 11": "NH1" <-> "NH2" Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 11": "NH1" <-> "NH2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 11": "NH1" <-> "NH2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 11": "NH1" <-> "NH2" Residue "N PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "R PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4060 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "B" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "C" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "E" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "F" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "G" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "H" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "I" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "J" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "K" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "L" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "M" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "N" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "O" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "Q" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "R" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "S" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "T" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 202 Unusual residues: {'NH2': 1} Classifications: {'peptide': 27, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 26} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.31, per 1000 atoms: 0.57 Number of scatterers: 4060 At special positions: 0 Unit cell: (90, 103.5, 42.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 800 8.00 N 760 7.00 C 2500 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: 1.52 Conformation dependent library (CDL) restraints added in 816.1 milliseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 640 1.28 - 1.35: 740 1.35 - 1.41: 461 1.41 - 1.48: 667 1.48 - 1.54: 1592 Bond restraints: 4100 Sorted by residual: bond pdb=" CB VAL P 32 " pdb=" CG2 VAL P 32 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.23e+00 bond pdb=" CB VAL O 32 " pdb=" CG2 VAL O 32 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CB VAL H 32 " pdb=" CG2 VAL H 32 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB VAL D 32 " pdb=" CG2 VAL D 32 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB VAL K 32 " pdb=" CG2 VAL K 32 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.90e+00 ... (remaining 4095 not shown) Histogram of bond angle deviations from ideal: 106.04 - 111.10: 1667 111.10 - 116.15: 857 116.15 - 121.21: 1753 121.21 - 126.26: 1263 126.26 - 131.31: 20 Bond angle restraints: 5560 Sorted by residual: angle pdb=" C VAL H 32 " pdb=" N GLY H 33 " pdb=" CA GLY H 33 " ideal model delta sigma weight residual 120.11 123.44 -3.33 1.51e+00 4.39e-01 4.87e+00 angle pdb=" N GLY O 33 " pdb=" CA GLY O 33 " pdb=" C GLY O 33 " ideal model delta sigma weight residual 113.48 116.70 -3.22 1.46e+00 4.69e-01 4.86e+00 angle pdb=" C VAL L 32 " pdb=" N GLY L 33 " pdb=" CA GLY L 33 " ideal model delta sigma weight residual 120.11 123.44 -3.33 1.51e+00 4.39e-01 4.86e+00 angle pdb=" C VAL G 32 " pdb=" N GLY G 33 " pdb=" CA GLY G 33 " ideal model delta sigma weight residual 120.11 123.43 -3.32 1.51e+00 4.39e-01 4.82e+00 angle pdb=" C VAL D 32 " pdb=" N GLY D 33 " pdb=" CA GLY D 33 " ideal model delta sigma weight residual 120.11 123.41 -3.30 1.51e+00 4.39e-01 4.78e+00 ... (remaining 5555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.87: 1849 8.87 - 17.75: 291 17.75 - 26.62: 83 26.62 - 35.50: 37 35.50 - 44.37: 20 Dihedral angle restraints: 2280 sinusoidal: 780 harmonic: 1500 Sorted by residual: dihedral pdb=" CA LEU E 16 " pdb=" C LEU E 16 " pdb=" N VAL E 17 " pdb=" CA VAL E 17 " ideal model delta harmonic sigma weight residual -180.00 -166.78 -13.22 0 5.00e+00 4.00e-02 6.99e+00 dihedral pdb=" CA LEU F 16 " pdb=" C LEU F 16 " pdb=" N VAL F 17 " pdb=" CA VAL F 17 " ideal model delta harmonic sigma weight residual -180.00 -166.79 -13.21 0 5.00e+00 4.00e-02 6.99e+00 dihedral pdb=" CA LEU A 16 " pdb=" C LEU A 16 " pdb=" N VAL A 17 " pdb=" CA VAL A 17 " ideal model delta harmonic sigma weight residual 180.00 -166.79 -13.21 0 5.00e+00 4.00e-02 6.98e+00 ... (remaining 2277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 340 0.038 - 0.076: 211 0.076 - 0.115: 52 0.115 - 0.153: 26 0.153 - 0.191: 11 Chirality restraints: 640 Sorted by residual: chirality pdb=" CG LEU P 27 " pdb=" CB LEU P 27 " pdb=" CD1 LEU P 27 " pdb=" CD2 LEU P 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CB VAL H 32 " pdb=" CA VAL H 32 " pdb=" CG1 VAL H 32 " pdb=" CG2 VAL H 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CB VAL L 32 " pdb=" CA VAL L 32 " pdb=" CG1 VAL L 32 " pdb=" CG2 VAL L 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 637 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 37 " 0.009 2.00e-02 2.50e+03 8.17e-03 1.34e+00 pdb=" CG TYR P 37 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR P 37 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR P 37 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR P 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR P 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR P 37 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 37 " 0.007 2.00e-02 2.50e+03 6.15e-03 7.55e-01 pdb=" CG TYR K 37 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR K 37 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR K 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR K 37 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR K 37 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR K 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 37 " 0.007 2.00e-02 2.50e+03 6.12e-03 7.50e-01 pdb=" CG TYR C 37 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR C 37 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 37 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 37 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 37 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 37 " -0.001 2.00e-02 2.50e+03 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 1973 2.97 - 3.45: 3623 3.45 - 3.93: 7314 3.93 - 4.42: 7888 4.42 - 4.90: 13625 Nonbonded interactions: 34423 Sorted by model distance: nonbonded pdb=" OG1 THR I 36 " pdb=" O HOH I 101 " model vdw 2.485 2.440 nonbonded pdb=" OG1 THR J 36 " pdb=" O HOH J 101 " model vdw 2.488 2.440 nonbonded pdb=" OG1 THR M 36 " pdb=" O HOH M 101 " model vdw 2.521 2.440 nonbonded pdb=" OG1 THR R 36 " pdb=" O HOH R 101 " model vdw 2.525 2.440 nonbonded pdb=" OG1 THR E 36 " pdb=" O HOH E 101 " model vdw 2.539 2.440 ... (remaining 34418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 1.070 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: 0.000 Extract box with map and model: 5.420 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 14.050 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4100 Z= 0.231 Angle : 0.662 5.048 5560 Z= 0.380 Chirality : 0.055 0.191 640 Planarity : 0.002 0.008 740 Dihedral : 11.454 44.371 1320 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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: -2.90 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 18 PHE 0.009 0.002 PHE M 15 TYR 0.020 0.003 TYR P 37 ARG 0.002 0.001 ARG M 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.450 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1861 time to fit residues: 13.9877 Evaluate side-chains 39 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 35 ASN C 35 ASN D 35 ASN E 22 ASN E 35 ASN F 22 ASN F 35 ASN G 35 ASN H 35 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 35 ASN J 14 ASN J 22 ASN J 35 ASN K 31 ASN K 35 ASN L 35 ASN M 22 ASN M 35 ASN N 22 ASN N 35 ASN P 35 ASN Q 14 ASN Q 22 ASN Q 35 ASN R 22 ASN R 35 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4100 Z= 0.224 Angle : 0.605 5.029 5560 Z= 0.339 Chirality : 0.052 0.157 640 Planarity : 0.002 0.012 740 Dihedral : 5.610 14.133 560 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.23 % Allowed : 5.23 % Favored : 94.55 % 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: -2.81 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS Q 18 PHE 0.010 0.001 PHE J 23 TYR 0.014 0.002 TYR P 37 ARG 0.001 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.451 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.2103 time to fit residues: 12.0667 Evaluate side-chains 35 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 32 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN D 35 ASN F 14 ASN G 35 ASN I 14 ASN M 14 ASN P 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4100 Z= 0.208 Angle : 0.568 4.679 5560 Z= 0.318 Chirality : 0.050 0.183 640 Planarity : 0.002 0.012 740 Dihedral : 5.616 14.024 560 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.45 % Allowed : 7.05 % Favored : 92.50 % 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: -2.85 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 18 PHE 0.010 0.001 PHE J 23 TYR 0.014 0.002 TYR D 37 ARG 0.001 0.000 ARG R 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.471 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.2060 time to fit residues: 10.4619 Evaluate side-chains 32 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 32 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 30.0000 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN D 35 ASN G 35 ASN K 31 ASN K 35 ASN R 14 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4100 Z= 0.284 Angle : 0.620 5.042 5560 Z= 0.347 Chirality : 0.054 0.210 640 Planarity : 0.003 0.012 740 Dihedral : 5.822 15.136 560 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.45 % Allowed : 7.50 % Favored : 92.05 % 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: -2.94 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS J 18 PHE 0.012 0.002 PHE P 23 TYR 0.015 0.003 TYR C 37 ARG 0.001 0.000 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.467 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.2074 time to fit residues: 10.5258 Evaluate side-chains 36 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 31 ASN K 35 ASN P 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4100 Z= 0.256 Angle : 0.597 4.972 5560 Z= 0.334 Chirality : 0.053 0.212 640 Planarity : 0.002 0.012 740 Dihedral : 5.751 15.798 560 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.45 % Allowed : 7.27 % Favored : 92.27 % 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: -2.96 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 18 PHE 0.012 0.002 PHE Q 23 TYR 0.015 0.002 TYR C 37 ARG 0.001 0.000 ARG R 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.554 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.2070 time to fit residues: 10.0183 Evaluate side-chains 32 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4100 Z= 0.183 Angle : 0.539 5.369 5560 Z= 0.300 Chirality : 0.049 0.195 640 Planarity : 0.002 0.011 740 Dihedral : 5.558 15.425 560 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.45 % Allowed : 7.95 % Favored : 91.59 % 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: -2.92 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 18 PHE 0.014 0.001 PHE P 23 TYR 0.013 0.002 TYR D 37 ARG 0.001 0.000 ARG S 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.428 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.2130 time to fit residues: 10.9553 Evaluate side-chains 35 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 35 ASN N 14 ASN P 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4100 Z= 0.195 Angle : 0.553 5.356 5560 Z= 0.306 Chirality : 0.050 0.200 640 Planarity : 0.002 0.007 740 Dihedral : 5.598 15.990 560 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.45 % Allowed : 8.64 % Favored : 90.91 % 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: -2.98 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 18 PHE 0.014 0.001 PHE S 23 TYR 0.014 0.002 TYR D 37 ARG 0.001 0.000 ARG S 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.479 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.2069 time to fit residues: 9.7903 Evaluate side-chains 33 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 35 optimal weight: 0.0010 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4100 Z= 0.165 Angle : 0.531 6.106 5560 Z= 0.292 Chirality : 0.048 0.197 640 Planarity : 0.002 0.008 740 Dihedral : 5.484 15.582 560 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.23 % Allowed : 8.86 % Favored : 90.91 % 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: -2.98 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.014 0.001 PHE L 23 TYR 0.012 0.002 TYR D 37 ARG 0.001 0.000 ARG S 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.459 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1991 time to fit residues: 9.4833 Evaluate side-chains 36 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 0.0870 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 35 ASN P 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 4100 Z= 0.109 Angle : 0.492 6.526 5560 Z= 0.268 Chirality : 0.046 0.174 640 Planarity : 0.001 0.008 740 Dihedral : 5.236 15.165 560 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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: -2.97 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 18 PHE 0.013 0.001 PHE G 23 TYR 0.012 0.002 TYR R 37 ARG 0.000 0.000 ARG S 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.494 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2144 time to fit residues: 9.8212 Evaluate side-chains 32 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 35 ASN L 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4100 Z= 0.304 Angle : 0.628 5.405 5560 Z= 0.347 Chirality : 0.055 0.233 640 Planarity : 0.003 0.010 740 Dihedral : 5.768 16.595 560 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.23 % Allowed : 9.32 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 18 PHE 0.013 0.002 PHE Q 23 TYR 0.017 0.003 TYR D 37 ARG 0.001 0.000 ARG S 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.428 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.2136 time to fit residues: 9.3259 Evaluate side-chains 33 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN K 35 ASN P 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.146241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084597 restraints weight = 3998.737| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.45 r_work: 0.3216 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4100 Z= 0.245 Angle : 0.587 6.260 5560 Z= 0.324 Chirality : 0.052 0.229 640 Planarity : 0.002 0.009 740 Dihedral : 5.663 16.488 560 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.23 % Allowed : 9.09 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 18 PHE 0.013 0.002 PHE S 23 TYR 0.015 0.003 TYR D 37 ARG 0.001 0.000 ARG S 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.06 seconds wall clock time: 23 minutes 32.68 seconds (1412.68 seconds total)