Starting phenix.real_space_refine on Fri Aug 2 21:43:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxb_18717/08_2024/8qxb_18717.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxb_18717/08_2024/8qxb_18717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxb_18717/08_2024/8qxb_18717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxb_18717/08_2024/8qxb_18717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxb_18717/08_2024/8qxb_18717.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxb_18717/08_2024/8qxb_18717.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 3348 2.51 5 N 990 2.21 5 O 1080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5544 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "B" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "D" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "E" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "F" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "G" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "H" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "K" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "L" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "M" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "O" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "P" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "Q" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Time building chain proxies: 3.05, per 1000 atoms: 0.55 Number of scatterers: 5544 At special positions: 0 Unit cell: (109.2, 104, 46.8, 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 126 16.00 O 1080 8.00 N 990 7.00 C 3348 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: 1.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.021A pdb=" N SER A 317 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER D 317 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER G 317 " --> pdb=" O ILE J 318 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER J 317 " --> pdb=" O ILE M 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER M 317 " --> pdb=" O ILE P 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 331 removed outlier: 5.905A pdb=" N ALA A 328 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN D 331 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 330 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA D 328 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN G 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 330 " --> pdb=" O GLN G 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA G 328 " --> pdb=" O ALA J 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN J 331 " --> pdb=" O ALA G 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU G 330 " --> pdb=" O GLN J 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA J 328 " --> pdb=" O ALA M 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN M 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU J 330 " --> pdb=" O GLN M 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA M 328 " --> pdb=" O ALA P 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN P 331 " --> pdb=" O ALA M 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU M 330 " --> pdb=" O GLN P 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 318 removed outlier: 6.022A pdb=" N SER B 317 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER E 317 " --> pdb=" O ILE H 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER H 317 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER K 317 " --> pdb=" O ILE N 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER N 317 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 331 removed outlier: 5.905A pdb=" N ALA B 328 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN E 331 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU B 330 " --> pdb=" O GLN E 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA E 328 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN H 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU E 330 " --> pdb=" O GLN H 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA H 328 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN K 331 " --> pdb=" O ALA H 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU H 330 " --> pdb=" O GLN K 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA K 328 " --> pdb=" O ALA N 329 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN N 331 " --> pdb=" O ALA K 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU K 330 " --> pdb=" O GLN N 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA N 328 " --> pdb=" O ALA Q 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN Q 331 " --> pdb=" O ALA N 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU N 330 " --> pdb=" O GLN Q 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.022A pdb=" N SER C 317 " --> pdb=" O ILE F 318 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER F 317 " --> pdb=" O ILE I 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER I 317 " --> pdb=" O ILE L 318 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER L 317 " --> pdb=" O ILE O 318 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER O 317 " --> pdb=" O ILE R 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 331 removed outlier: 5.905A pdb=" N ALA C 328 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN F 331 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 330 " --> pdb=" O GLN F 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA F 328 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN I 331 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU F 330 " --> pdb=" O GLN I 331 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA I 328 " --> pdb=" O ALA L 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN L 331 " --> pdb=" O ALA I 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU I 330 " --> pdb=" O GLN L 331 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA L 328 " --> pdb=" O ALA O 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN O 331 " --> pdb=" O ALA L 328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU L 330 " --> pdb=" O GLN O 331 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA O 328 " --> pdb=" O ALA R 329 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLN R 331 " --> pdb=" O ALA O 328 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU O 330 " --> pdb=" O GLN R 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 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: 0.15 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 990 1.32 - 1.44: 1440 1.44 - 1.57: 2934 1.57 - 1.69: 0 1.69 - 1.82: 252 Bond restraints: 5616 Sorted by residual: bond pdb=" C SER J 317 " pdb=" O SER J 317 " ideal model delta sigma weight residual 1.235 1.193 0.043 1.13e-02 7.83e+03 1.41e+01 bond pdb=" C SER C 317 " pdb=" O SER C 317 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.13e-02 7.83e+03 1.41e+01 bond pdb=" C SER A 317 " pdb=" O SER A 317 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.13e-02 7.83e+03 1.41e+01 bond pdb=" C SER M 317 " pdb=" O SER M 317 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.13e-02 7.83e+03 1.41e+01 bond pdb=" C SER D 317 " pdb=" O SER D 317 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.13e-02 7.83e+03 1.41e+01 ... (remaining 5611 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.75: 230 104.75 - 112.12: 2110 112.12 - 119.49: 2633 119.49 - 126.86: 2425 126.86 - 134.24: 72 Bond angle restraints: 7470 Sorted by residual: angle pdb=" N GLN O 327 " pdb=" CA GLN O 327 " pdb=" C GLN O 327 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.32e+01 angle pdb=" N GLN H 327 " pdb=" CA GLN H 327 " pdb=" C GLN H 327 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.31e+01 angle pdb=" N GLN N 327 " pdb=" CA GLN N 327 " pdb=" C GLN N 327 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.31e+01 angle pdb=" N GLN J 327 " pdb=" CA GLN J 327 " pdb=" C GLN J 327 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.31e+01 angle pdb=" N GLN G 327 " pdb=" CA GLN G 327 " pdb=" C GLN G 327 " ideal model delta sigma weight residual 111.07 104.92 6.15 1.07e+00 8.73e-01 3.30e+01 ... (remaining 7465 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 15.30: 2880 15.30 - 30.56: 234 30.56 - 45.83: 108 45.83 - 61.10: 36 61.10 - 76.36: 36 Dihedral angle restraints: 3294 sinusoidal: 1170 harmonic: 2124 Sorted by residual: dihedral pdb=" C PHE L 316 " pdb=" N PHE L 316 " pdb=" CA PHE L 316 " pdb=" CB PHE L 316 " ideal model delta harmonic sigma weight residual -122.60 -114.29 -8.31 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C PHE F 316 " pdb=" N PHE F 316 " pdb=" CA PHE F 316 " pdb=" CB PHE F 316 " ideal model delta harmonic sigma weight residual -122.60 -114.29 -8.31 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C PHE K 316 " pdb=" N PHE K 316 " pdb=" CA PHE K 316 " pdb=" CB PHE K 316 " ideal model delta harmonic sigma weight residual -122.60 -114.30 -8.30 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 3291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 242 0.053 - 0.106: 208 0.106 - 0.160: 162 0.160 - 0.213: 54 0.213 - 0.266: 54 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA TRP G 334 " pdb=" N TRP G 334 " pdb=" C TRP G 334 " pdb=" CB TRP G 334 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA TRP M 334 " pdb=" N TRP M 334 " pdb=" C TRP M 334 " pdb=" CB TRP M 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA TRP D 334 " pdb=" N TRP D 334 " pdb=" C TRP D 334 " pdb=" CB TRP D 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.76e+00 ... (remaining 717 not shown) Planarity restraints: 1026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO Q 320 " 0.014 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C PRO Q 320 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO Q 320 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA Q 321 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 320 " 0.014 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C PRO H 320 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO H 320 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA H 321 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO M 320 " -0.014 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C PRO M 320 " 0.052 2.00e-02 2.50e+03 pdb=" O PRO M 320 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA M 321 " -0.018 2.00e-02 2.50e+03 ... (remaining 1023 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2559 2.99 - 3.47: 5265 3.47 - 3.94: 9271 3.94 - 4.42: 10560 4.42 - 4.90: 20365 Nonbonded interactions: 48020 Sorted by model distance: nonbonded pdb=" N PRO B 320 " pdb=" O PRO B 320 " model vdw 2.508 2.496 nonbonded pdb=" N PRO A 320 " pdb=" O PRO A 320 " model vdw 2.509 2.496 nonbonded pdb=" N PRO P 320 " pdb=" O PRO P 320 " model vdw 2.509 2.496 nonbonded pdb=" N PRO C 320 " pdb=" O PRO C 320 " model vdw 2.509 2.496 nonbonded pdb=" N PRO H 320 " pdb=" O PRO H 320 " model vdw 2.509 2.496 ... (remaining 48015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 0.830 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.680 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 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 0.046 5616 Z= 1.055 Angle : 2.276 6.656 7470 Z= 1.679 Chirality : 0.115 0.266 720 Planarity : 0.010 0.030 1026 Dihedral : 18.192 76.362 1962 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % 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: -3.90 (0.18), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.14), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.010 TRP O 334 PHE 0.006 0.003 PHE Q 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8052 (ttt) cc_final: 0.7843 (ttp) REVERT: A 323 MET cc_start: 0.6862 (ttm) cc_final: 0.6644 (ttt) REVERT: A 334 TRP cc_start: 0.6777 (p90) cc_final: 0.5394 (m100) REVERT: B 307 MET cc_start: 0.8224 (ttt) cc_final: 0.7898 (ttp) REVERT: B 334 TRP cc_start: 0.6702 (p90) cc_final: 0.5018 (m100) REVERT: C 334 TRP cc_start: 0.6713 (p90) cc_final: 0.4824 (m100) REVERT: E 305 SER cc_start: 0.6314 (m) cc_final: 0.6104 (m) REVERT: E 307 MET cc_start: 0.8478 (ttt) cc_final: 0.8100 (ttt) REVERT: F 307 MET cc_start: 0.8411 (ttt) cc_final: 0.8168 (ttt) REVERT: F 334 TRP cc_start: 0.6975 (p90) cc_final: 0.6749 (p90) REVERT: H 307 MET cc_start: 0.8441 (ttt) cc_final: 0.8208 (ttm) REVERT: I 305 SER cc_start: 0.6337 (m) cc_final: 0.6030 (m) REVERT: K 305 SER cc_start: 0.6294 (m) cc_final: 0.6076 (m) REVERT: L 307 MET cc_start: 0.8216 (ttt) cc_final: 0.7777 (ttt) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1331 time to fit residues: 57.9657 Evaluate side-chains 227 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 327 GLN C 327 GLN E 343 GLN G 343 GLN ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN I 343 GLN I 344 GLN ** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 GLN O 343 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5616 Z= 0.149 Angle : 0.695 7.017 7470 Z= 0.351 Chirality : 0.039 0.116 720 Planarity : 0.003 0.030 1026 Dihedral : 5.427 14.674 792 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.68 % Allowed : 41.95 % Favored : 55.36 % 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: -4.04 (0.20), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.15), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 334 PHE 0.007 0.001 PHE L 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 252 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 336 MET cc_start: 0.5705 (ttm) cc_final: 0.5490 (ttt) REVERT: C 337 MET cc_start: 0.5876 (ppp) cc_final: 0.5507 (ppp) REVERT: D 336 MET cc_start: 0.8078 (ttp) cc_final: 0.7731 (ttt) REVERT: E 322 MET cc_start: 0.5886 (mmm) cc_final: 0.4856 (ptp) REVERT: P 336 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6601 (ttt) REVERT: R 336 MET cc_start: 0.6646 (ttp) cc_final: 0.6396 (ttt) outliers start: 14 outliers final: 5 residues processed: 254 average time/residue: 0.1301 time to fit residues: 44.5488 Evaluate side-chains 218 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 212 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain R residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 343 GLN ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 5616 Z= 0.420 Angle : 0.900 7.706 7470 Z= 0.477 Chirality : 0.044 0.151 720 Planarity : 0.005 0.035 1026 Dihedral : 6.553 19.136 792 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.36 % Allowed : 35.82 % Favored : 58.81 % 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: -4.65 (0.15), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.11), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP G 334 PHE 0.019 0.003 PHE R 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 MET cc_start: 0.6637 (ttt) cc_final: 0.6386 (ttt) REVERT: C 307 MET cc_start: 0.8482 (ttm) cc_final: 0.8214 (ttp) REVERT: C 311 MET cc_start: 0.8726 (ptp) cc_final: 0.8402 (ptp) REVERT: E 322 MET cc_start: 0.6133 (mmm) cc_final: 0.5256 (ptt) REVERT: F 322 MET cc_start: 0.6313 (mmt) cc_final: 0.4493 (ptt) REVERT: G 336 MET cc_start: 0.8440 (ttp) cc_final: 0.8116 (ttp) REVERT: H 311 MET cc_start: 0.8830 (ptp) cc_final: 0.8480 (ptp) REVERT: J 336 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8164 (ttt) REVERT: M 307 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8412 (ttp) REVERT: M 336 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8251 (ttp) REVERT: P 322 MET cc_start: 0.5849 (mtt) cc_final: 0.5401 (mtt) REVERT: Q 307 MET cc_start: 0.8485 (ttm) cc_final: 0.8215 (ttt) REVERT: R 313 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8584 (m-80) REVERT: R 336 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7650 (ttt) outliers start: 28 outliers final: 19 residues processed: 217 average time/residue: 0.1257 time to fit residues: 36.9833 Evaluate side-chains 211 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 336 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 313 PHE Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 336 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 GLN ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5616 Z= 0.199 Angle : 0.712 7.248 7470 Z= 0.358 Chirality : 0.039 0.118 720 Planarity : 0.004 0.036 1026 Dihedral : 5.677 17.072 792 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.60 % Allowed : 34.48 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.15), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.11), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 334 PHE 0.016 0.002 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 MET cc_start: 0.4902 (mmt) cc_final: 0.4400 (ptp) REVERT: C 307 MET cc_start: 0.8449 (ttm) cc_final: 0.8166 (ttp) REVERT: C 311 MET cc_start: 0.8594 (ptp) cc_final: 0.8351 (ptp) REVERT: C 323 MET cc_start: 0.6427 (ttt) cc_final: 0.6161 (ttt) REVERT: E 307 MET cc_start: 0.8687 (ttm) cc_final: 0.8267 (ttm) REVERT: E 322 MET cc_start: 0.5711 (mmm) cc_final: 0.4996 (ptp) REVERT: F 322 MET cc_start: 0.5224 (mmt) cc_final: 0.4579 (ptp) REVERT: G 336 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8029 (ttp) REVERT: H 311 MET cc_start: 0.8727 (ptp) cc_final: 0.8382 (ptp) REVERT: H 322 MET cc_start: 0.6715 (mmt) cc_final: 0.6499 (mmt) REVERT: H 336 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8108 (ttt) REVERT: J 327 GLN cc_start: 0.7485 (tm-30) cc_final: 0.7239 (tm-30) REVERT: J 336 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8186 (ttt) REVERT: L 327 GLN cc_start: 0.7270 (tm-30) cc_final: 0.7052 (tm-30) REVERT: M 336 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8164 (ttp) REVERT: N 337 MET cc_start: 0.7040 (mmt) cc_final: 0.6739 (mtt) REVERT: P 322 MET cc_start: 0.5612 (mtt) cc_final: 0.5269 (mtt) REVERT: Q 307 MET cc_start: 0.8476 (ttm) cc_final: 0.8174 (ttp) REVERT: R 322 MET cc_start: 0.5791 (mtt) cc_final: 0.5231 (mtt) outliers start: 24 outliers final: 17 residues processed: 223 average time/residue: 0.1330 time to fit residues: 40.3805 Evaluate side-chains 219 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 336 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN G 343 GLN ** I 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 GLN ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5616 Z= 0.159 Angle : 0.677 7.480 7470 Z= 0.334 Chirality : 0.039 0.120 720 Planarity : 0.003 0.030 1026 Dihedral : 5.239 15.465 792 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.60 % Allowed : 35.25 % Favored : 60.15 % 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: -4.39 (0.15), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 334 PHE 0.013 0.002 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 322 MET cc_start: 0.4609 (mmt) cc_final: 0.4326 (ptp) REVERT: C 307 MET cc_start: 0.8345 (ttm) cc_final: 0.8138 (ttp) REVERT: D 336 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8189 (ttp) REVERT: E 322 MET cc_start: 0.5575 (mmm) cc_final: 0.4856 (ptp) REVERT: E 323 MET cc_start: 0.6836 (ttt) cc_final: 0.6584 (ttt) REVERT: G 336 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8016 (ttp) REVERT: H 336 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7978 (ttt) REVERT: J 322 MET cc_start: 0.6708 (mmt) cc_final: 0.6471 (mmt) REVERT: J 336 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8165 (ttt) REVERT: P 322 MET cc_start: 0.5244 (mtt) cc_final: 0.5035 (mtt) REVERT: Q 307 MET cc_start: 0.8493 (ttm) cc_final: 0.8172 (ttp) REVERT: R 322 MET cc_start: 0.5761 (mtt) cc_final: 0.5232 (mtt) outliers start: 24 outliers final: 17 residues processed: 221 average time/residue: 0.1367 time to fit residues: 40.9812 Evaluate side-chains 218 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN D 327 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 346 GLN ** I 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5616 Z= 0.213 Angle : 0.716 7.562 7470 Z= 0.362 Chirality : 0.039 0.118 720 Planarity : 0.003 0.026 1026 Dihedral : 5.464 16.387 792 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.75 % Allowed : 35.25 % Favored : 59.00 % 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: -4.49 (0.15), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 334 PHE 0.013 0.002 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 0.578 Fit side-chains REVERT: A 322 MET cc_start: 0.4388 (mmt) cc_final: 0.4064 (ptp) REVERT: E 322 MET cc_start: 0.5705 (mmm) cc_final: 0.5199 (ptp) REVERT: G 327 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7222 (tm-30) REVERT: G 336 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8030 (ttp) REVERT: G 337 MET cc_start: 0.7328 (mmt) cc_final: 0.6973 (mmt) REVERT: H 311 MET cc_start: 0.8965 (ptp) cc_final: 0.8621 (ptp) REVERT: J 336 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8030 (ttt) REVERT: L 337 MET cc_start: 0.7534 (mmt) cc_final: 0.7246 (mmt) REVERT: Q 307 MET cc_start: 0.8531 (ttm) cc_final: 0.8231 (ttp) outliers start: 30 outliers final: 21 residues processed: 206 average time/residue: 0.1352 time to fit residues: 38.0686 Evaluate side-chains 218 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 344 GLN Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN D 327 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN K 312 ASN M 346 GLN ** N 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.7143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5616 Z= 0.126 Angle : 0.658 8.077 7470 Z= 0.320 Chirality : 0.038 0.117 720 Planarity : 0.002 0.019 1026 Dihedral : 4.955 19.070 792 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.36 % Allowed : 34.29 % Favored : 60.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 334 PHE 0.011 0.001 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 206 time to evaluate : 0.590 Fit side-chains REVERT: D 322 MET cc_start: 0.5999 (mmt) cc_final: 0.4022 (ptp) REVERT: D 336 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8107 (ttp) REVERT: E 322 MET cc_start: 0.5337 (mmm) cc_final: 0.5002 (ptp) REVERT: G 336 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7846 (ttp) REVERT: G 337 MET cc_start: 0.7238 (mmt) cc_final: 0.6964 (mmt) REVERT: H 336 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7815 (ttt) REVERT: I 307 MET cc_start: 0.8381 (tpp) cc_final: 0.8179 (ttm) REVERT: J 336 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7875 (ttt) REVERT: L 336 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7768 (ttp) REVERT: M 322 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6057 (mmt) REVERT: Q 307 MET cc_start: 0.8506 (ttm) cc_final: 0.8198 (ttp) REVERT: R 322 MET cc_start: 0.5660 (mtt) cc_final: 0.5282 (mtt) outliers start: 28 outliers final: 21 residues processed: 213 average time/residue: 0.1319 time to fit residues: 38.3315 Evaluate side-chains 224 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 197 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 332 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 322 MET Chi-restraints excluded: chain M residue 346 GLN Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 312 ASN Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 0.0020 chunk 64 optimal weight: 0.0020 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 312 ASN ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5616 Z= 0.115 Angle : 0.669 8.115 7470 Z= 0.321 Chirality : 0.038 0.117 720 Planarity : 0.002 0.015 1026 Dihedral : 4.809 18.808 792 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 5.36 % Allowed : 34.87 % Favored : 59.77 % 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: -4.38 (0.17), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.13), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 334 PHE 0.011 0.001 PHE C 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 0.549 Fit side-chains REVERT: D 322 MET cc_start: 0.5534 (mmt) cc_final: 0.4357 (ptp) REVERT: D 336 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8051 (ttp) REVERT: G 336 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7822 (ttp) REVERT: H 336 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7780 (ttt) REVERT: J 336 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7809 (ttt) REVERT: M 322 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6097 (mmt) REVERT: Q 307 MET cc_start: 0.8510 (ttm) cc_final: 0.8200 (ttp) outliers start: 28 outliers final: 22 residues processed: 207 average time/residue: 0.1316 time to fit residues: 36.9933 Evaluate side-chains 218 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 332 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 322 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 312 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 312 ASN Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN D 327 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.7435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5616 Z= 0.218 Angle : 0.752 8.424 7470 Z= 0.374 Chirality : 0.040 0.119 720 Planarity : 0.003 0.016 1026 Dihedral : 5.398 19.139 792 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.36 % Allowed : 34.10 % Favored : 60.54 % 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: -4.74 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 334 PHE 0.014 0.002 PHE Q 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 0.512 Fit side-chains REVERT: D 322 MET cc_start: 0.5773 (mmt) cc_final: 0.4060 (ptp) REVERT: G 336 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7923 (ttp) REVERT: H 336 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7661 (ttt) REVERT: J 336 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7879 (ttt) REVERT: M 322 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6207 (mmt) REVERT: Q 307 MET cc_start: 0.8527 (ttm) cc_final: 0.8131 (ttp) outliers start: 28 outliers final: 22 residues processed: 201 average time/residue: 0.1262 time to fit residues: 34.7192 Evaluate side-chains 213 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 332 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 322 MET Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 312 ASN Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 332 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN ** K 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 346 GLN ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 346 GLN ** Q 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.7595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5616 Z= 0.142 Angle : 0.707 8.891 7470 Z= 0.338 Chirality : 0.039 0.117 720 Planarity : 0.002 0.018 1026 Dihedral : 5.052 21.959 792 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.75 % Allowed : 33.52 % Favored : 60.73 % 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: -4.72 (0.16), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.12), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 334 PHE 0.010 0.001 PHE C 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 0.568 Fit side-chains REVERT: A 307 MET cc_start: 0.8287 (ttm) cc_final: 0.8070 (ttp) REVERT: D 322 MET cc_start: 0.5352 (mmt) cc_final: 0.4370 (ptp) REVERT: G 336 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7935 (ttp) REVERT: H 336 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7779 (ttt) REVERT: J 336 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7732 (ttt) REVERT: K 339 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7392 (ptp) REVERT: M 322 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6132 (mmt) REVERT: P 336 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6697 (ttt) REVERT: P 337 MET cc_start: 0.6259 (mtt) cc_final: 0.5865 (mtt) REVERT: Q 307 MET cc_start: 0.8406 (ttm) cc_final: 0.8167 (ttp) outliers start: 30 outliers final: 22 residues processed: 206 average time/residue: 0.1265 time to fit residues: 35.6583 Evaluate side-chains 218 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 336 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 332 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 339 MET Chi-restraints excluded: chain L residue 305 SER Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 322 MET Chi-restraints excluded: chain M residue 346 GLN Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 305 SER Chi-restraints excluded: chain P residue 312 ASN Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 334 TRP Chi-restraints excluded: chain P residue 336 MET Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain Q residue 332 SER Chi-restraints excluded: chain Q residue 334 TRP Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 334 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.0470 chunk 15 optimal weight: 0.0770 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 GLN H 346 GLN ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 346 GLN N 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.333909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 146)---------------| | r_work = 0.4958 r_free = 0.4958 target = 0.239927 restraints weight = 8700.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 87)----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.237617 restraints weight = 14151.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 82)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.237848 restraints weight = 14937.942| |-----------------------------------------------------------------------------| r_work (final): 0.4752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.7845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5616 Z= 0.108 Angle : 0.689 9.527 7470 Z= 0.321 Chirality : 0.038 0.116 720 Planarity : 0.002 0.015 1026 Dihedral : 4.677 23.780 792 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.17 % Allowed : 35.06 % Favored : 59.77 % 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: -4.60 (0.17), residues: 774 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.13), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 334 PHE 0.011 0.001 PHE C 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1647.00 seconds wall clock time: 29 minutes 45.54 seconds (1785.54 seconds total)