Starting phenix.real_space_refine on Sun Mar 10 14:55:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/03_2024/8ot1_17166.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/03_2024/8ot1_17166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/03_2024/8ot1_17166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/03_2024/8ot1_17166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/03_2024/8ot1_17166.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/03_2024/8ot1_17166.pdb" } resolution = 2.59 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1596 2.51 5 N 432 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2460 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "D" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "E" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "F" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "G" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "H" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "I" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "K" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Time building chain proxies: 1.62, per 1000 atoms: 0.66 Number of scatterers: 2460 At special positions: 0 Unit cell: (77.522, 83.126, 43.898, 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 12 16.00 O 420 8.00 N 432 7.00 C 1596 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: 0.87 Conformation dependent library (CDL) restraints added in 438.8 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 24 removed outlier: 6.384A pdb=" N LYS A 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA C 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE A 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP C 23 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU A 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS C 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA E 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP E 23 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU C 22 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS E 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA G 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE E 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP G 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU E 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS G 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE I 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA I 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE G 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP I 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU G 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS I 16 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE K 19 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL I 18 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA K 21 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE I 20 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP K 23 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU I 22 " --> pdb=" O ASP K 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 24 removed outlier: 6.384A pdb=" N LYS B 16 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA D 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE B 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP D 23 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU B 22 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS D 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA F 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 20 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP F 23 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU D 22 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS F 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE H 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA H 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE F 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP H 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU F 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS H 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE J 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA J 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE H 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP J 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU H 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS J 16 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE L 19 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL J 18 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA L 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE J 20 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP L 23 " --> pdb=" O PHE J 20 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N GLU J 22 " --> pdb=" O ASP L 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 0.05 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 540 1.33 - 1.45: 492 1.45 - 1.57: 1440 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 2496 Sorted by residual: bond pdb=" CA GLY A 33 " pdb=" C GLY A 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" CA GLY B 33 " pdb=" C GLY B 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" CA GLY I 33 " pdb=" C GLY I 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.51e+01 bond pdb=" CA GLY J 33 " pdb=" C GLY J 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.51e+01 bond pdb=" CA GLY D 33 " pdb=" C GLY D 33 " ideal model delta sigma weight residual 1.514 1.460 0.054 1.41e-02 5.03e+03 1.49e+01 ... (remaining 2491 not shown) Histogram of bond angle deviations from ideal: 102.12 - 107.96: 204 107.96 - 113.81: 1128 113.81 - 119.65: 986 119.65 - 125.49: 982 125.49 - 131.34: 36 Bond angle restraints: 3336 Sorted by residual: angle pdb=" CA GLY F 38 " pdb=" C GLY F 38 " pdb=" O GLY F 38 " ideal model delta sigma weight residual 122.23 118.11 4.12 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY E 38 " pdb=" C GLY E 38 " pdb=" O GLY E 38 " ideal model delta sigma weight residual 122.23 118.11 4.12 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY H 38 " pdb=" C GLY H 38 " pdb=" O GLY H 38 " ideal model delta sigma weight residual 122.23 118.12 4.11 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY G 38 " pdb=" C GLY G 38 " pdb=" O GLY G 38 " ideal model delta sigma weight residual 122.23 118.12 4.11 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY L 38 " pdb=" C GLY L 38 " pdb=" O GLY L 38 " ideal model delta sigma weight residual 122.23 118.12 4.11 6.90e-01 2.10e+00 3.55e+01 ... (remaining 3331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.97: 1152 12.97 - 25.93: 156 25.93 - 38.90: 24 38.90 - 51.86: 36 51.86 - 64.83: 24 Dihedral angle restraints: 1392 sinusoidal: 516 harmonic: 876 Sorted by residual: dihedral pdb=" CA GLU K 22 " pdb=" CB GLU K 22 " pdb=" CG GLU K 22 " pdb=" CD GLU K 22 " ideal model delta sinusoidal sigma weight residual -60.00 -118.23 58.23 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLU L 22 " pdb=" CB GLU L 22 " pdb=" CG GLU L 22 " pdb=" CD GLU L 22 " ideal model delta sinusoidal sigma weight residual -60.00 -118.23 58.23 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLU I 22 " pdb=" CB GLU I 22 " pdb=" CG GLU I 22 " pdb=" CD GLU I 22 " ideal model delta sinusoidal sigma weight residual -60.00 -118.22 58.22 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1389 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.053: 84 0.053 - 0.104: 60 0.104 - 0.155: 132 0.155 - 0.207: 84 0.207 - 0.258: 24 Chirality restraints: 384 Sorted by residual: chirality pdb=" CA ILE E 31 " pdb=" N ILE E 31 " pdb=" C ILE E 31 " pdb=" CB ILE E 31 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE F 31 " pdb=" N ILE F 31 " pdb=" C ILE F 31 " pdb=" CB ILE F 31 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE L 31 " pdb=" N ILE L 31 " pdb=" C ILE L 31 " pdb=" CB ILE L 31 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 381 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 34 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LEU G 34 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU G 34 " -0.021 2.00e-02 2.50e+03 pdb=" N MET G 35 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 34 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LEU H 34 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU H 34 " 0.021 2.00e-02 2.50e+03 pdb=" N MET H 35 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 34 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU K 34 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU K 34 " -0.021 2.00e-02 2.50e+03 pdb=" N MET K 35 " -0.019 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 1042 2.96 - 3.45: 2198 3.45 - 3.93: 4190 3.93 - 4.41: 4504 4.41 - 4.90: 8910 Nonbonded interactions: 20844 Sorted by model distance: nonbonded pdb=" N LEU B 34 " pdb=" O LEU B 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU A 34 " pdb=" O LEU A 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU L 34 " pdb=" O LEU L 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU K 34 " pdb=" O LEU K 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU E 34 " pdb=" O LEU E 34 " model vdw 2.477 2.496 ... (remaining 20839 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' } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.360 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.790 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 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 : 0.013 0.055 2496 Z= 0.995 Angle : 2.400 11.686 3336 Z= 1.683 Chirality : 0.128 0.258 384 Planarity : 0.012 0.032 420 Dihedral : 17.351 64.826 840 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 23.81 % Favored : 76.19 % 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: -3.37 (0.27), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 14 PHE 0.021 0.005 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.6085 time to fit residues: 49.2105 Evaluate side-chains 76 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS C 14 HIS D 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2496 Z= 0.147 Angle : 0.659 3.718 3336 Z= 0.371 Chirality : 0.052 0.118 384 Planarity : 0.003 0.014 420 Dihedral : 4.295 10.890 324 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 31.75 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.28), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 14 PHE 0.010 0.002 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.270 Fit side-chains REVERT: E 35 MET cc_start: 0.6526 (mtp) cc_final: 0.6144 (mtt) REVERT: F 35 MET cc_start: 0.6530 (mtp) cc_final: 0.6147 (mtt) outliers start: 8 outliers final: 2 residues processed: 82 average time/residue: 0.6056 time to fit residues: 51.6597 Evaluate side-chains 74 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 7 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2496 Z= 0.116 Angle : 0.611 3.971 3336 Z= 0.338 Chirality : 0.051 0.125 384 Planarity : 0.002 0.013 420 Dihedral : 4.269 10.171 324 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.59 % Allowed : 23.81 % Favored : 74.60 % 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: -2.18 (0.36), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 14 PHE 0.007 0.001 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.287 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 70 average time/residue: 0.6911 time to fit residues: 50.2045 Evaluate side-chains 74 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2496 Z= 0.222 Angle : 0.718 4.426 3336 Z= 0.394 Chirality : 0.050 0.139 384 Planarity : 0.003 0.011 420 Dihedral : 5.023 12.550 324 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 8.33 % Allowed : 19.44 % Favored : 72.22 % 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: -2.06 (0.37), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 14 PHE 0.014 0.003 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.282 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 85 average time/residue: 0.5827 time to fit residues: 51.5936 Evaluate side-chains 84 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2496 Z= 0.127 Angle : 0.662 5.362 3336 Z= 0.358 Chirality : 0.052 0.136 384 Planarity : 0.003 0.016 420 Dihedral : 4.709 10.247 324 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.75 % Allowed : 21.83 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.39), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 14 PHE 0.007 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.225 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 83 average time/residue: 0.5910 time to fit residues: 51.0857 Evaluate side-chains 80 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain L residue 23 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2496 Z= 0.126 Angle : 0.680 5.235 3336 Z= 0.364 Chirality : 0.052 0.133 384 Planarity : 0.003 0.018 420 Dihedral : 4.604 10.614 324 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.56 % Allowed : 21.83 % Favored : 72.62 % 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: -1.86 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 14 PHE 0.008 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.283 Fit side-chains REVERT: E 35 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6199 (mtt) REVERT: F 35 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.6187 (mtt) REVERT: G 35 MET cc_start: 0.6640 (mtp) cc_final: 0.6285 (mtt) REVERT: H 35 MET cc_start: 0.6653 (mtp) cc_final: 0.6384 (mtt) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.6518 time to fit residues: 50.1165 Evaluate side-chains 84 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain L residue 23 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2496 Z= 0.150 Angle : 0.739 6.572 3336 Z= 0.392 Chirality : 0.052 0.133 384 Planarity : 0.003 0.020 420 Dihedral : 4.715 10.809 324 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.35 % Allowed : 23.41 % Favored : 70.24 % 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: -1.96 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 14 PHE 0.008 0.001 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.280 Fit side-chains REVERT: E 35 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6235 (mtt) REVERT: F 35 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6228 (mtt) REVERT: G 35 MET cc_start: 0.6730 (mtp) cc_final: 0.6374 (mtt) REVERT: H 35 MET cc_start: 0.6730 (mtp) cc_final: 0.6413 (mtt) outliers start: 16 outliers final: 8 residues processed: 72 average time/residue: 0.6657 time to fit residues: 49.7454 Evaluate side-chains 76 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain L residue 23 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.0270 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2496 Z= 0.138 Angle : 0.749 7.248 3336 Z= 0.395 Chirality : 0.052 0.129 384 Planarity : 0.004 0.026 420 Dihedral : 4.626 10.003 324 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.16 % Allowed : 26.98 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 14 PHE 0.007 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.276 Fit side-chains REVERT: E 35 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.6231 (mtt) REVERT: F 35 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6199 (mtt) REVERT: G 35 MET cc_start: 0.6740 (mtp) cc_final: 0.6394 (mtt) REVERT: H 35 MET cc_start: 0.6741 (mtp) cc_final: 0.6435 (mtt) outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.6912 time to fit residues: 50.8735 Evaluate side-chains 79 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain L residue 23 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2496 Z= 0.176 Angle : 0.849 7.292 3336 Z= 0.447 Chirality : 0.053 0.133 384 Planarity : 0.003 0.027 420 Dihedral : 4.820 11.281 324 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.56 % Allowed : 28.17 % Favored : 66.27 % 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: -2.01 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 14 PHE 0.009 0.001 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.282 Fit side-chains REVERT: E 35 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6248 (mtt) REVERT: F 35 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6273 (mtt) REVERT: G 35 MET cc_start: 0.6788 (mtp) cc_final: 0.6424 (mtt) REVERT: H 35 MET cc_start: 0.6789 (mtp) cc_final: 0.6524 (mtt) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.6912 time to fit residues: 50.2115 Evaluate side-chains 76 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 0.0060 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2496 Z= 0.149 Angle : 0.840 7.798 3336 Z= 0.439 Chirality : 0.053 0.129 384 Planarity : 0.005 0.031 420 Dihedral : 4.722 11.593 324 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.76 % Allowed : 28.17 % Favored : 67.06 % 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: -1.92 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 14 PHE 0.006 0.001 PHE D 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.279 Fit side-chains REVERT: E 35 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6219 (mtt) REVERT: F 35 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.6253 (mtt) REVERT: G 35 MET cc_start: 0.6764 (mtp) cc_final: 0.6350 (mtt) REVERT: H 35 MET cc_start: 0.6763 (mtp) cc_final: 0.6472 (mtt) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 0.7009 time to fit residues: 50.1611 Evaluate side-chains 75 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5172 r_free = 0.5172 target = 0.182056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.156453 restraints weight = 3134.182| |-----------------------------------------------------------------------------| r_work (start): 0.4892 rms_B_bonded: 3.52 r_work: 0.4796 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2496 Z= 0.186 Angle : 0.906 8.078 3336 Z= 0.474 Chirality : 0.053 0.134 384 Planarity : 0.003 0.028 420 Dihedral : 4.942 12.688 324 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.37 % Allowed : 29.37 % Favored : 66.27 % 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: -1.96 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 14 PHE 0.009 0.002 PHE D 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1568.74 seconds wall clock time: 28 minutes 18.07 seconds (1698.07 seconds total)