Starting phenix.real_space_refine on Sat Apr 6 00:54:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq5_17105/04_2024/8oq5_17105.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq5_17105/04_2024/8oq5_17105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq5_17105/04_2024/8oq5_17105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq5_17105/04_2024/8oq5_17105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq5_17105/04_2024/8oq5_17105.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq5_17105/04_2024/8oq5_17105.pdb" } resolution = 2.4 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 36 5.16 5 C 4128 2.51 5 N 1044 2.21 5 O 1320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 6": "OD1" <-> "OD2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 6": "OD1" <-> "OD2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 6": "OD1" <-> "OD2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 6": "OD1" <-> "OD2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 6": "OD1" <-> "OD2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 6": "OD1" <-> "OD2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 6": "OD1" <-> "OD2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 6": "OD1" <-> "OD2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 6": "OD1" <-> "OD2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I GLU 33": "OE1" <-> "OE2" Residue "I TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 6": "OD1" <-> "OD2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L GLU 33": "OE1" <-> "OE2" Residue "L TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 6": "OD1" <-> "OD2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M GLU 33": "OE1" <-> "OE2" Residue "M TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 6": "OD1" <-> "OD2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 27": "OE1" <-> "OE2" Residue "N GLU 33": "OE1" <-> "OE2" Residue "N TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6528 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "B" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "C" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "D" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "E" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "F" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "G" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "H" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "I" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "L" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Time building chain proxies: 3.78, per 1000 atoms: 0.58 Number of scatterers: 6528 At special positions: 0 Unit cell: (117.52, 91.52, 49.92, 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 36 16.00 O 1320 8.00 N 1044 7.00 C 4128 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: 2.44 Conformation dependent library (CDL) restraints added in 1.4 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.681A pdb=" N ASP A 6 " --> pdb=" O MET C 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP C 6 " --> pdb=" O MET E 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP E 6 " --> pdb=" O MET G 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP G 6 " --> pdb=" O MET I 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP I 6 " --> pdb=" O MET M 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.252A pdb=" N LEU A 10 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU C 10 " --> pdb=" O PHE E 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU E 10 " --> pdb=" O PHE G 11 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU G 10 " --> pdb=" O PHE I 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU I 10 " --> pdb=" O PHE M 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 21 removed outlier: 6.092A pdb=" N THR A 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR C 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR E 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR I 19 " --> pdb=" O GLU M 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 49 removed outlier: 8.747A pdb=" N GLU A 47 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLU C 47 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLU E 47 " --> pdb=" O GLN G 48 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N GLU G 47 " --> pdb=" O GLN I 48 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLU I 47 " --> pdb=" O GLN M 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA7, first strand: chain 'A' and resid 60 through 64 Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 7 removed outlier: 6.681A pdb=" N ASP B 6 " --> pdb=" O MET D 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP D 6 " --> pdb=" O MET F 7 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP F 6 " --> pdb=" O MET H 7 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP H 6 " --> pdb=" O MET L 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP L 6 " --> pdb=" O MET N 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.251A pdb=" N LEU B 10 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU D 10 " --> pdb=" O PHE F 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU F 10 " --> pdb=" O PHE H 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU H 10 " --> pdb=" O PHE L 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU L 10 " --> pdb=" O PHE N 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 21 removed outlier: 6.093A pdb=" N THR B 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR D 19 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR F 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR H 19 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR L 19 " --> pdb=" O GLU N 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB3, first strand: chain 'B' and resid 46 through 49 removed outlier: 8.746A pdb=" N GLU B 47 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N GLU D 47 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N GLU F 47 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N GLU H 47 " --> pdb=" O GLN L 48 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N GLU L 47 " --> pdb=" O GLN N 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 64 70 hydrogen bonds defined for protein. 210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1116 1.29 - 1.42: 1659 1.42 - 1.56: 3764 1.56 - 1.69: 25 1.69 - 1.82: 72 Bond restraints: 6636 Sorted by residual: bond pdb=" C TYR I 21 " pdb=" O TYR I 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.45e+01 bond pdb=" C TYR N 21 " pdb=" O TYR N 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.45e+01 bond pdb=" C TYR F 21 " pdb=" O TYR F 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.44e+01 bond pdb=" C TYR H 21 " pdb=" O TYR H 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.44e+01 bond pdb=" C TYR C 21 " pdb=" O TYR C 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.43e+01 ... (remaining 6631 not shown) Histogram of bond angle deviations from ideal: 100.47 - 106.68: 298 106.68 - 112.89: 2798 112.89 - 119.10: 2810 119.10 - 125.31: 2920 125.31 - 131.52: 78 Bond angle restraints: 8904 Sorted by residual: angle pdb=" N ILE H 34 " pdb=" CA ILE H 34 " pdb=" C ILE H 34 " ideal model delta sigma weight residual 107.37 115.95 -8.58 1.48e+00 4.57e-01 3.36e+01 angle pdb=" N ILE G 34 " pdb=" CA ILE G 34 " pdb=" C ILE G 34 " ideal model delta sigma weight residual 107.37 115.95 -8.58 1.48e+00 4.57e-01 3.36e+01 angle pdb=" N ILE I 34 " pdb=" CA ILE I 34 " pdb=" C ILE I 34 " ideal model delta sigma weight residual 107.37 115.95 -8.58 1.48e+00 4.57e-01 3.36e+01 angle pdb=" N ILE D 34 " pdb=" CA ILE D 34 " pdb=" C ILE D 34 " ideal model delta sigma weight residual 107.37 115.94 -8.57 1.48e+00 4.57e-01 3.35e+01 angle pdb=" N ILE N 34 " pdb=" CA ILE N 34 " pdb=" C ILE N 34 " ideal model delta sigma weight residual 107.37 115.93 -8.56 1.48e+00 4.57e-01 3.35e+01 ... (remaining 8899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.61: 3252 9.61 - 19.22: 384 19.22 - 28.84: 204 28.84 - 38.45: 96 38.45 - 48.06: 84 Dihedral angle restraints: 4020 sinusoidal: 1620 harmonic: 2400 Sorted by residual: dihedral pdb=" CA ALA L 40 " pdb=" C ALA L 40 " pdb=" N TYR L 41 " pdb=" CA TYR L 41 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ALA B 40 " pdb=" C ALA B 40 " pdb=" N TYR B 41 " pdb=" CA TYR B 41 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ALA C 40 " pdb=" C ALA C 40 " pdb=" N TYR C 41 " pdb=" CA TYR C 41 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 4017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 312 0.047 - 0.094: 288 0.094 - 0.141: 237 0.141 - 0.187: 87 0.187 - 0.234: 60 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA VAL D 61 " pdb=" N VAL D 61 " pdb=" C VAL D 61 " pdb=" CB VAL D 61 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA VAL L 61 " pdb=" N VAL L 61 " pdb=" C VAL L 61 " pdb=" CB VAL L 61 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL F 61 " pdb=" N VAL F 61 " pdb=" C VAL F 61 " pdb=" CB VAL F 61 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 981 not shown) Planarity restraints: 1140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 16 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLN I 16 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN I 16 " -0.021 2.00e-02 2.50e+03 pdb=" N SER I 17 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 67 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LEU N 67 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU N 67 " 0.021 2.00e-02 2.50e+03 pdb=" N MET N 68 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 16 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C GLN G 16 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN G 16 " -0.021 2.00e-02 2.50e+03 pdb=" N SER G 17 " -0.020 2.00e-02 2.50e+03 ... (remaining 1137 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 3421 2.99 - 3.47: 5989 3.47 - 3.95: 11952 3.95 - 4.42: 13817 4.42 - 4.90: 25285 Nonbonded interactions: 60464 Sorted by model distance: nonbonded pdb=" OG SER B 66 " pdb=" O PHE D 63 " model vdw 2.517 2.440 nonbonded pdb=" OG SER H 66 " pdb=" O PHE L 63 " model vdw 2.517 2.440 nonbonded pdb=" OG SER C 66 " pdb=" O PHE E 63 " model vdw 2.518 2.440 nonbonded pdb=" OG SER E 66 " pdb=" O PHE G 63 " model vdw 2.518 2.440 nonbonded pdb=" OG SER F 66 " pdb=" O PHE H 63 " model vdw 2.518 2.440 ... (remaining 60459 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 'L' selection = chain 'M' selection = chain 'N' } 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: 1.900 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: 6.570 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.660 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:16.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.015 0.069 6636 Z= 1.005 Angle : 2.049 8.581 8904 Z= 1.453 Chirality : 0.100 0.234 984 Planarity : 0.011 0.033 1140 Dihedral : 14.254 48.059 2460 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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: -5.16 (0.16), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.12), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 46 PHE 0.016 0.005 PHE I 11 TYR 0.031 0.006 TYR L 21 ARG 0.001 0.000 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 0.724 Fit side-chains REVERT: N 50 THR cc_start: 0.8229 (p) cc_final: 0.8028 (p) outliers start: 0 outliers final: 3 residues processed: 313 average time/residue: 1.2353 time to fit residues: 404.5052 Evaluate side-chains 242 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain N residue 6 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN F 35 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 13 GLN H 35 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN I 35 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN L 35 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 35 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6636 Z= 0.228 Angle : 0.668 7.861 8904 Z= 0.337 Chirality : 0.042 0.125 984 Planarity : 0.004 0.043 1140 Dihedral : 6.472 23.428 858 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.69 % Allowed : 17.49 % Favored : 78.83 % 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: -4.30 (0.20), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.15), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 46 PHE 0.010 0.002 PHE E 11 TYR 0.014 0.002 TYR G 21 ARG 0.005 0.002 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 273 time to evaluate : 0.847 Fit side-chains REVERT: A 69 ASN cc_start: 0.8260 (t0) cc_final: 0.8028 (t0) REVERT: B 28 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7706 (mptt) REVERT: E 24 ASP cc_start: 0.8149 (m-30) cc_final: 0.7913 (m-30) REVERT: G 30 LYS cc_start: 0.8217 (mtpp) cc_final: 0.8016 (mtpt) REVERT: M 18 MET cc_start: 0.8015 (ttm) cc_final: 0.7654 (ttp) outliers start: 27 outliers final: 4 residues processed: 288 average time/residue: 1.1323 time to fit residues: 342.2564 Evaluate side-chains 244 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 239 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6636 Z= 0.383 Angle : 0.775 7.333 8904 Z= 0.389 Chirality : 0.046 0.141 984 Planarity : 0.005 0.046 1140 Dihedral : 6.846 24.578 852 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.87 % Allowed : 20.36 % Favored : 76.78 % 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: -3.87 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 46 PHE 0.014 0.002 PHE N 42 TYR 0.014 0.003 TYR G 21 ARG 0.004 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 0.777 Fit side-chains REVERT: B 41 TYR cc_start: 0.8341 (m-80) cc_final: 0.8083 (m-80) REVERT: C 33 GLU cc_start: 0.7012 (tt0) cc_final: 0.6742 (tm-30) REVERT: E 24 ASP cc_start: 0.8341 (m-30) cc_final: 0.8128 (m-30) REVERT: F 28 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7941 (mptt) REVERT: G 71 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6856 (mt-10) REVERT: I 43 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: M 18 MET cc_start: 0.8046 (ttm) cc_final: 0.7710 (ttp) REVERT: M 67 LEU cc_start: 0.7812 (mp) cc_final: 0.7560 (mp) outliers start: 21 outliers final: 9 residues processed: 256 average time/residue: 1.2477 time to fit residues: 333.9375 Evaluate side-chains 244 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 233 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.0470 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6636 Z= 0.199 Angle : 0.641 7.176 8904 Z= 0.319 Chirality : 0.041 0.121 984 Planarity : 0.003 0.033 1140 Dihedral : 6.029 21.169 852 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.01 % Allowed : 22.95 % Favored : 74.04 % 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: -3.70 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 46 PHE 0.005 0.001 PHE I 42 TYR 0.012 0.002 TYR E 21 ARG 0.002 0.001 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 253 time to evaluate : 0.817 Fit side-chains REVERT: C 33 GLU cc_start: 0.6969 (tt0) cc_final: 0.6669 (tm-30) REVERT: E 24 ASP cc_start: 0.8244 (m-30) cc_final: 0.7969 (m-30) REVERT: F 28 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8002 (mptt) REVERT: M 18 MET cc_start: 0.8045 (ttm) cc_final: 0.7740 (ttp) REVERT: M 67 LEU cc_start: 0.7729 (mp) cc_final: 0.7473 (mp) outliers start: 22 outliers final: 6 residues processed: 264 average time/residue: 1.2825 time to fit residues: 354.3247 Evaluate side-chains 254 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 247 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 37 GLN D 37 GLN F 37 GLN H 37 GLN L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6636 Z= 0.247 Angle : 0.659 7.822 8904 Z= 0.332 Chirality : 0.042 0.128 984 Planarity : 0.004 0.038 1140 Dihedral : 6.043 21.021 852 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.73 % Allowed : 25.96 % Favored : 71.31 % 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: -3.58 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 46 PHE 0.009 0.001 PHE B 11 TYR 0.013 0.002 TYR G 41 ARG 0.003 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 242 time to evaluate : 0.710 Fit side-chains REVERT: A 43 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: C 33 GLU cc_start: 0.6965 (tt0) cc_final: 0.6714 (tm-30) REVERT: C 70 LEU cc_start: 0.9136 (tt) cc_final: 0.8934 (tp) REVERT: E 24 ASP cc_start: 0.8341 (m-30) cc_final: 0.8024 (m-30) REVERT: F 28 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7955 (mptt) REVERT: M 18 MET cc_start: 0.8044 (ttm) cc_final: 0.7738 (ttp) REVERT: M 43 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: M 67 LEU cc_start: 0.7798 (mp) cc_final: 0.7572 (mp) outliers start: 20 outliers final: 8 residues processed: 253 average time/residue: 1.4282 time to fit residues: 376.6968 Evaluate side-chains 252 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 241 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain M residue 43 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.0270 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6636 Z= 0.211 Angle : 0.642 8.530 8904 Z= 0.321 Chirality : 0.041 0.127 984 Planarity : 0.003 0.034 1140 Dihedral : 5.800 19.877 852 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.73 % Allowed : 26.37 % Favored : 70.90 % 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: -3.49 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 46 PHE 0.007 0.001 PHE B 11 TYR 0.013 0.002 TYR G 41 ARG 0.002 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 242 time to evaluate : 0.827 Fit side-chains REVERT: A 43 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: C 33 GLU cc_start: 0.6961 (tt0) cc_final: 0.6685 (tm-30) REVERT: E 24 ASP cc_start: 0.8302 (m-30) cc_final: 0.7948 (m-30) REVERT: F 28 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7979 (mptt) REVERT: M 18 MET cc_start: 0.8058 (ttm) cc_final: 0.7731 (ttp) outliers start: 20 outliers final: 10 residues processed: 252 average time/residue: 1.2725 time to fit residues: 334.9633 Evaluate side-chains 247 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 235 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6636 Z= 0.277 Angle : 0.678 8.667 8904 Z= 0.342 Chirality : 0.042 0.134 984 Planarity : 0.004 0.040 1140 Dihedral : 6.036 20.803 852 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.60 % Allowed : 26.23 % Favored : 71.17 % 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: -3.51 (0.22), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 46 PHE 0.007 0.001 PHE B 11 TYR 0.011 0.002 TYR L 14 ARG 0.003 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 0.803 Fit side-chains REVERT: A 43 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: C 33 GLU cc_start: 0.6970 (tt0) cc_final: 0.6713 (tm-30) REVERT: E 24 ASP cc_start: 0.8346 (m-30) cc_final: 0.8055 (m-30) REVERT: F 28 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7936 (mptt) REVERT: M 18 MET cc_start: 0.8061 (ttm) cc_final: 0.7752 (ttp) outliers start: 19 outliers final: 11 residues processed: 249 average time/residue: 1.2512 time to fit residues: 325.6063 Evaluate side-chains 251 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 238 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6636 Z= 0.307 Angle : 0.708 8.783 8904 Z= 0.356 Chirality : 0.043 0.136 984 Planarity : 0.004 0.042 1140 Dihedral : 6.167 21.459 852 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.73 % Allowed : 26.64 % Favored : 70.63 % 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: -3.55 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.008 0.001 PHE B 11 TYR 0.012 0.002 TYR L 14 ARG 0.003 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 0.761 Fit side-chains REVERT: A 43 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: C 33 GLU cc_start: 0.6985 (tt0) cc_final: 0.6733 (tm-30) REVERT: E 24 ASP cc_start: 0.8380 (m-30) cc_final: 0.8092 (m-30) REVERT: F 28 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7969 (mptt) REVERT: M 18 MET cc_start: 0.8062 (ttm) cc_final: 0.7767 (ttp) outliers start: 20 outliers final: 12 residues processed: 254 average time/residue: 1.2689 time to fit residues: 336.9206 Evaluate side-chains 254 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 240 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6636 Z= 0.230 Angle : 0.676 8.844 8904 Z= 0.336 Chirality : 0.042 0.129 984 Planarity : 0.003 0.037 1140 Dihedral : 5.861 19.883 852 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.05 % Allowed : 27.32 % Favored : 70.63 % 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: -3.57 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 46 PHE 0.007 0.001 PHE B 11 TYR 0.016 0.002 TYR M 41 ARG 0.002 0.001 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 237 time to evaluate : 0.849 Fit side-chains REVERT: A 43 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: C 33 GLU cc_start: 0.6950 (tt0) cc_final: 0.6698 (tm-30) REVERT: E 24 ASP cc_start: 0.8336 (m-30) cc_final: 0.7992 (m-30) REVERT: F 28 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7962 (mptt) REVERT: M 18 MET cc_start: 0.8087 (ttm) cc_final: 0.7745 (ttp) outliers start: 15 outliers final: 10 residues processed: 246 average time/residue: 1.2830 time to fit residues: 329.5785 Evaluate side-chains 249 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 237 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain I residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6636 Z= 0.297 Angle : 0.715 8.943 8904 Z= 0.357 Chirality : 0.043 0.133 984 Planarity : 0.004 0.041 1140 Dihedral : 6.101 20.809 852 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.32 % Allowed : 27.46 % Favored : 70.22 % 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: -3.61 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 46 PHE 0.008 0.001 PHE B 11 TYR 0.016 0.002 TYR M 41 ARG 0.003 0.001 ARG I 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 241 time to evaluate : 0.837 Fit side-chains REVERT: C 33 GLU cc_start: 0.6967 (tt0) cc_final: 0.6711 (tm-30) REVERT: E 24 ASP cc_start: 0.8370 (m-30) cc_final: 0.8074 (m-30) REVERT: F 28 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7931 (mptt) REVERT: M 18 MET cc_start: 0.8058 (ttm) cc_final: 0.7756 (ttp) outliers start: 17 outliers final: 12 residues processed: 252 average time/residue: 1.2761 time to fit residues: 335.9847 Evaluate side-chains 252 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 239 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 70 LEU 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: 0.8980 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.116513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.107445 restraints weight = 7341.788| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.37 r_work: 0.3536 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6636 Z= 0.270 Angle : 0.706 10.065 8904 Z= 0.352 Chirality : 0.042 0.131 984 Planarity : 0.004 0.041 1140 Dihedral : 6.034 20.358 852 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.78 % Allowed : 28.28 % Favored : 69.95 % 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: -3.64 (0.21), residues: 792 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 46 PHE 0.008 0.001 PHE B 11 TYR 0.016 0.002 TYR M 41 ARG 0.003 0.001 ARG I 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4935.08 seconds wall clock time: 88 minutes 13.29 seconds (5293.29 seconds total)