Starting phenix.real_space_refine on Mon Mar 11 06:27:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/03_2024/8ehr_28150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/03_2024/8ehr_28150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/03_2024/8ehr_28150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/03_2024/8ehr_28150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/03_2024/8ehr_28150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/03_2024/8ehr_28150.pdb" } resolution = 3.2 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= 0.012 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 21 5.16 5 C 4606 2.51 5 N 1204 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A ASP 21": "OD1" <-> "OD2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 64": "OD1" <-> "OD2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E ASP 21": "OD1" <-> "OD2" Residue "E PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 64": "OD1" <-> "OD2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 2": "OE1" <-> "OE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 64": "OD1" <-> "OD2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 2": "OE1" <-> "OE2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G ASP 21": "OD1" <-> "OD2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 64": "OD1" <-> "OD2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7350 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "C" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "E" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "B" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "F" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "G" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Time building chain proxies: 4.40, per 1000 atoms: 0.60 Number of scatterers: 7350 At special positions: 0 Unit cell: (85.162, 84.084, 100.254, 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 21 16.00 O 1519 8.00 N 1204 7.00 C 4606 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: 2.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 19 sheets defined 4.1% alpha, 52.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 15 through 19 removed outlier: 5.097A pdb=" N GLN F 67 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL F 138 " --> pdb=" O GLN F 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 28 through 31 removed outlier: 8.122A pdb=" N VAL F 29 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 6 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU F 31 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR A 8 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL F 138 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN F 67 " --> pdb=" O VAL F 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 77 through 84 current: chain 'F' and resid 94 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.097A pdb=" N GLN A 67 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL A 138 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.882A pdb=" N THR A 39 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER B 10 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A 33 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL A 138 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN A 67 " --> pdb=" O VAL A 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 77 through 84 current: chain 'A' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.098A pdb=" N GLN G 67 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL G 138 " --> pdb=" O GLN G 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 28 through 31 removed outlier: 8.083A pdb=" N VAL G 29 " --> pdb=" O ASN C 4 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR C 6 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU G 31 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 8 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL G 138 " --> pdb=" O GLN G 67 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN G 67 " --> pdb=" O VAL G 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 77 through 84 current: chain 'G' and resid 94 through 96 Processing sheet with id=AA7, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AA8, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AA9, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.786A pdb=" N THR C 39 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 94 through 96 Processing sheet with id=AB2, first strand: chain 'D' and resid 15 through 19 removed outlier: 5.098A pdb=" N GLN D 67 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL D 138 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 28 through 31 removed outlier: 4.361A pdb=" N SER E 10 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL D 138 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN D 67 " --> pdb=" O VAL D 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 77 through 84 current: chain 'D' and resid 94 through 96 Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 34 removed outlier: 3.713A pdb=" N THR D 39 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.098A pdb=" N GLN E 67 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL E 138 " --> pdb=" O GLN E 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.738A pdb=" N THR E 39 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F 10 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR E 33 " --> pdb=" O SER F 10 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL E 138 " --> pdb=" O GLN E 67 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN E 67 " --> pdb=" O VAL E 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 77 through 84 current: chain 'E' and resid 94 through 96 Processing sheet with id=AB7, first strand: chain 'B' and resid 15 through 19 removed outlier: 5.097A pdb=" N GLN B 67 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL B 138 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.751A pdb=" N THR B 39 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER G 10 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR B 33 " --> pdb=" O SER G 10 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL B 138 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN B 67 " --> pdb=" O VAL B 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 77 through 84 current: chain 'B' and resid 94 through 96 Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.693A pdb=" N THR F 39 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 33 through 34 removed outlier: 3.717A pdb=" N THR G 39 " --> pdb=" O SER G 34 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 705 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: 1.94 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2389 1.34 - 1.45: 691 1.45 - 1.57: 4333 1.57 - 1.68: 0 1.68 - 1.80: 42 Bond restraints: 7455 Sorted by residual: bond pdb=" C SER E 34 " pdb=" O SER E 34 " ideal model delta sigma weight residual 1.244 1.221 0.022 1.10e-02 8.26e+03 4.09e+00 bond pdb=" CA ALA C 32 " pdb=" C ALA C 32 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.18e-02 7.18e+03 3.78e+00 bond pdb=" C SER D 34 " pdb=" O SER D 34 " ideal model delta sigma weight residual 1.240 1.219 0.021 1.14e-02 7.69e+03 3.44e+00 bond pdb=" N TYR E 33 " pdb=" CA TYR E 33 " ideal model delta sigma weight residual 1.456 1.435 0.021 1.23e-02 6.61e+03 2.97e+00 bond pdb=" C SER F 34 " pdb=" O SER F 34 " ideal model delta sigma weight residual 1.240 1.221 0.019 1.14e-02 7.69e+03 2.92e+00 ... (remaining 7450 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.24: 249 107.24 - 113.92: 4525 113.92 - 120.61: 2429 120.61 - 127.30: 2933 127.30 - 133.99: 63 Bond angle restraints: 10199 Sorted by residual: angle pdb=" C SER A 34 " pdb=" N PRO A 35 " pdb=" CA PRO A 35 " ideal model delta sigma weight residual 119.05 126.55 -7.50 1.11e+00 8.12e-01 4.56e+01 angle pdb=" C SER C 34 " pdb=" N PRO C 35 " pdb=" CA PRO C 35 " ideal model delta sigma weight residual 119.05 125.46 -6.41 1.11e+00 8.12e-01 3.34e+01 angle pdb=" C SER F 34 " pdb=" N PRO F 35 " pdb=" CA PRO F 35 " ideal model delta sigma weight residual 119.05 125.32 -6.27 1.11e+00 8.12e-01 3.19e+01 angle pdb=" C SER G 34 " pdb=" N PRO G 35 " pdb=" CA PRO G 35 " ideal model delta sigma weight residual 119.05 124.85 -5.80 1.11e+00 8.12e-01 2.73e+01 angle pdb=" C SER E 34 " pdb=" N PRO E 35 " pdb=" CA PRO E 35 " ideal model delta sigma weight residual 119.05 124.79 -5.74 1.11e+00 8.12e-01 2.68e+01 ... (remaining 10194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 4211 16.53 - 33.06: 206 33.06 - 49.59: 77 49.59 - 66.12: 14 66.12 - 82.65: 14 Dihedral angle restraints: 4522 sinusoidal: 1575 harmonic: 2947 Sorted by residual: dihedral pdb=" N MET C 46 " pdb=" CA MET C 46 " pdb=" CB MET C 46 " pdb=" CG MET C 46 " ideal model delta sinusoidal sigma weight residual -180.00 -138.60 -41.40 3 1.50e+01 4.44e-03 7.41e+00 dihedral pdb=" N MET E 46 " pdb=" CA MET E 46 " pdb=" CB MET E 46 " pdb=" CG MET E 46 " ideal model delta sinusoidal sigma weight residual -180.00 -138.62 -41.38 3 1.50e+01 4.44e-03 7.40e+00 dihedral pdb=" N MET D 46 " pdb=" CA MET D 46 " pdb=" CB MET D 46 " pdb=" CG MET D 46 " ideal model delta sinusoidal sigma weight residual 180.00 -138.65 -41.35 3 1.50e+01 4.44e-03 7.40e+00 ... (remaining 4519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1035 0.043 - 0.086: 104 0.086 - 0.129: 155 0.129 - 0.172: 4 0.172 - 0.214: 4 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA SER A 37 " pdb=" N SER A 37 " pdb=" C SER A 37 " pdb=" CB SER A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA SER F 37 " pdb=" N SER F 37 " pdb=" C SER F 37 " pdb=" CB SER F 37 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA SER E 37 " pdb=" N SER E 37 " pdb=" C SER E 37 " pdb=" CB SER E 37 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 1299 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 31 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C LEU D 31 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU D 31 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA D 32 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 31 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LEU C 31 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU C 31 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA C 32 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 31 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C LEU A 31 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU A 31 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 32 " 0.014 2.00e-02 2.50e+03 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 2657 2.88 - 3.38: 6088 3.38 - 3.89: 11512 3.89 - 4.39: 12825 4.39 - 4.90: 23520 Nonbonded interactions: 56602 Sorted by model distance: nonbonded pdb=" OD2 ASP C 21 " pdb=" ND2 ASN C 23 " model vdw 2.374 2.520 nonbonded pdb=" OD2 ASP A 21 " pdb=" ND2 ASN A 23 " model vdw 2.374 2.520 nonbonded pdb=" OD2 ASP E 21 " pdb=" ND2 ASN E 23 " model vdw 2.375 2.520 nonbonded pdb=" OD2 ASP G 21 " pdb=" ND2 ASN G 23 " model vdw 2.375 2.520 nonbonded pdb=" OD2 ASP D 21 " pdb=" ND2 ASN D 23 " model vdw 2.375 2.520 ... (remaining 56597 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' } 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: 0.370 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: 2.140 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.930 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.003 0.023 7455 Z= 0.193 Angle : 0.550 7.499 10199 Z= 0.352 Chirality : 0.045 0.214 1302 Planarity : 0.004 0.038 1295 Dihedral : 13.081 82.654 2618 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: 1.91 (0.25), residues: 385 loop : 0.86 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 84 HIS 0.002 0.001 HIS D 50 PHE 0.005 0.001 PHE G 40 TYR 0.008 0.001 TYR F 33 ARG 0.000 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.850 Fit side-chains REVERT: A 46 MET cc_start: 0.8745 (tpp) cc_final: 0.8212 (mmt) REVERT: A 53 ASP cc_start: 0.8173 (t0) cc_final: 0.7839 (t70) REVERT: A 56 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8174 (mttt) REVERT: A 72 LEU cc_start: 0.8296 (mt) cc_final: 0.8086 (mt) REVERT: C 48 GLN cc_start: 0.8850 (mt0) cc_final: 0.8552 (mt0) REVERT: D 53 ASP cc_start: 0.7824 (t0) cc_final: 0.7294 (t70) REVERT: D 56 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8096 (mttt) REVERT: D 90 SER cc_start: 0.8545 (t) cc_final: 0.8294 (p) REVERT: B 56 LYS cc_start: 0.8241 (mtpp) cc_final: 0.8028 (mtpt) REVERT: B 81 SER cc_start: 0.8514 (p) cc_final: 0.7864 (t) REVERT: B 144 THR cc_start: 0.8628 (t) cc_final: 0.8349 (m) REVERT: F 131 THR cc_start: 0.8458 (m) cc_final: 0.8194 (p) REVERT: G 128 THR cc_start: 0.7968 (p) cc_final: 0.7637 (t) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1885 time to fit residues: 38.0572 Evaluate side-chains 108 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN D 19 GLN B 19 GLN B 48 GLN G 19 GLN G 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7455 Z= 0.325 Angle : 0.585 7.700 10199 Z= 0.296 Chirality : 0.048 0.168 1302 Planarity : 0.004 0.030 1295 Dihedral : 5.013 35.011 1057 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.44 % Allowed : 8.79 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1008 helix: -5.31 (0.14), residues: 42 sheet: 1.84 (0.25), residues: 364 loop : 0.59 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 84 HIS 0.003 0.001 HIS F 50 PHE 0.007 0.001 PHE D 96 TYR 0.009 0.002 TYR A 33 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.925 Fit side-chains REVERT: A 46 MET cc_start: 0.8499 (tpp) cc_final: 0.7919 (mmt) REVERT: A 53 ASP cc_start: 0.8394 (t0) cc_final: 0.8161 (t70) REVERT: A 56 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8151 (mttt) REVERT: C 87 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7073 (mm-40) REVERT: D 53 ASP cc_start: 0.7871 (t0) cc_final: 0.7649 (t70) REVERT: D 56 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8345 (mtpt) REVERT: D 90 SER cc_start: 0.8486 (t) cc_final: 0.8274 (p) REVERT: E 46 MET cc_start: 0.9160 (tpp) cc_final: 0.8580 (mmt) REVERT: B 144 THR cc_start: 0.8709 (t) cc_final: 0.8436 (m) REVERT: G 128 THR cc_start: 0.7890 (p) cc_final: 0.7672 (t) outliers start: 20 outliers final: 15 residues processed: 126 average time/residue: 0.1786 time to fit residues: 31.0084 Evaluate side-chains 119 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN D 19 GLN D 23 ASN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 ASN B 19 GLN G 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 7455 Z= 0.119 Angle : 0.426 4.317 10199 Z= 0.217 Chirality : 0.044 0.149 1302 Planarity : 0.003 0.025 1295 Dihedral : 4.230 30.175 1057 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.08 % Allowed : 11.11 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1008 helix: -5.07 (0.19), residues: 42 sheet: 2.08 (0.25), residues: 364 loop : 0.70 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 84 HIS 0.002 0.001 HIS C 50 PHE 0.004 0.001 PHE G 40 TYR 0.004 0.001 TYR G 33 ARG 0.001 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.822 Fit side-chains REVERT: A 53 ASP cc_start: 0.8313 (t0) cc_final: 0.7926 (t70) REVERT: A 56 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8107 (mttt) REVERT: A 95 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7386 (mt-10) REVERT: D 56 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8327 (mtpt) REVERT: E 46 MET cc_start: 0.9141 (tpp) cc_final: 0.8466 (mmt) REVERT: B 144 THR cc_start: 0.8677 (t) cc_final: 0.8370 (m) REVERT: G 87 GLN cc_start: 0.7910 (mt0) cc_final: 0.7463 (mm-40) REVERT: G 128 THR cc_start: 0.7821 (p) cc_final: 0.7607 (t) outliers start: 17 outliers final: 9 residues processed: 128 average time/residue: 0.1709 time to fit residues: 30.6012 Evaluate side-chains 113 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN C 67 GLN D 19 GLN D 23 ASN B 19 GLN G 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7455 Z= 0.356 Angle : 0.591 7.834 10199 Z= 0.295 Chirality : 0.049 0.159 1302 Planarity : 0.003 0.028 1295 Dihedral : 5.132 37.696 1057 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.05 % Allowed : 13.68 % Favored : 83.27 % 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: 0.97 (0.24), residues: 1008 helix: -5.17 (0.18), residues: 42 sheet: 1.78 (0.25), residues: 364 loop : 0.44 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.006 0.001 PHE C 40 TYR 0.010 0.002 TYR A 33 ARG 0.001 0.000 ARG F 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.760 Fit side-chains REVERT: A 53 ASP cc_start: 0.8325 (t0) cc_final: 0.8113 (t0) REVERT: A 56 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8232 (mttt) REVERT: C 21 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7977 (p0) REVERT: D 53 ASP cc_start: 0.7871 (t70) cc_final: 0.7574 (t70) REVERT: D 56 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8492 (mtpt) REVERT: E 46 MET cc_start: 0.9197 (tpp) cc_final: 0.8627 (mmt) REVERT: B 144 THR cc_start: 0.8775 (t) cc_final: 0.8470 (m) REVERT: G 87 GLN cc_start: 0.8032 (mt0) cc_final: 0.7705 (mm-40) outliers start: 25 outliers final: 22 residues processed: 122 average time/residue: 0.1719 time to fit residues: 29.3256 Evaluate side-chains 128 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 80 optimal weight: 0.0040 chunk 65 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 overall best weight: 2.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7455 Z= 0.280 Angle : 0.534 6.764 10199 Z= 0.269 Chirality : 0.047 0.154 1302 Planarity : 0.003 0.028 1295 Dihedral : 5.030 39.906 1057 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.79 % Allowed : 14.53 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1008 helix: -5.06 (0.24), residues: 42 sheet: 1.78 (0.25), residues: 364 loop : 0.38 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE C 40 TYR 0.010 0.001 TYR A 33 ARG 0.001 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.834 Fit side-chains REVERT: A 53 ASP cc_start: 0.8380 (t0) cc_final: 0.8165 (t0) REVERT: A 56 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8228 (mttt) REVERT: C 21 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8004 (p0) REVERT: C 87 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7005 (mm-40) REVERT: D 53 ASP cc_start: 0.7875 (t70) cc_final: 0.7657 (t70) REVERT: D 56 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8587 (mtpt) REVERT: B 87 GLN cc_start: 0.8136 (mt0) cc_final: 0.7877 (mm-40) REVERT: B 144 THR cc_start: 0.8708 (t) cc_final: 0.8441 (m) REVERT: G 87 GLN cc_start: 0.7999 (mt0) cc_final: 0.7705 (mm-40) outliers start: 31 outliers final: 23 residues processed: 130 average time/residue: 0.1639 time to fit residues: 29.9899 Evaluate side-chains 130 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7455 Z= 0.242 Angle : 0.513 6.573 10199 Z= 0.258 Chirality : 0.046 0.152 1302 Planarity : 0.003 0.027 1295 Dihedral : 4.902 39.526 1057 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.42 % Allowed : 15.51 % Favored : 81.07 % 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: 0.95 (0.25), residues: 1008 helix: -4.96 (0.29), residues: 42 sheet: 1.82 (0.25), residues: 364 loop : 0.37 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE C 40 TYR 0.010 0.001 TYR A 33 ARG 0.001 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 0.831 Fit side-chains REVERT: A 53 ASP cc_start: 0.8337 (t0) cc_final: 0.8091 (t0) REVERT: A 56 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8227 (mttt) REVERT: A 87 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7830 (mm110) REVERT: C 87 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7032 (mm-40) REVERT: D 56 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8551 (mtpt) REVERT: B 21 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7834 (p0) REVERT: B 87 GLN cc_start: 0.8171 (mt0) cc_final: 0.7942 (mm-40) REVERT: B 144 THR cc_start: 0.8799 (t) cc_final: 0.8559 (m) REVERT: G 87 GLN cc_start: 0.8007 (mt0) cc_final: 0.7726 (mm-40) outliers start: 28 outliers final: 21 residues processed: 121 average time/residue: 0.1726 time to fit residues: 29.2467 Evaluate side-chains 127 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7455 Z= 0.221 Angle : 0.497 5.999 10199 Z= 0.250 Chirality : 0.046 0.151 1302 Planarity : 0.003 0.029 1295 Dihedral : 4.778 38.385 1057 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.79 % Allowed : 15.75 % Favored : 80.46 % 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: 1.00 (0.25), residues: 1008 helix: -4.92 (0.30), residues: 42 sheet: 1.87 (0.25), residues: 364 loop : 0.38 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE C 40 TYR 0.009 0.001 TYR A 33 ARG 0.001 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 0.820 Fit side-chains REVERT: A 53 ASP cc_start: 0.8314 (t0) cc_final: 0.8070 (t0) REVERT: A 56 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8235 (mttt) REVERT: A 67 GLN cc_start: 0.8591 (mt0) cc_final: 0.8135 (mt0) REVERT: A 87 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7833 (mm110) REVERT: C 21 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7951 (p0) REVERT: C 87 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7033 (mm-40) REVERT: D 56 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8513 (mtpt) REVERT: E 83 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8645 (m) REVERT: B 21 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7810 (p0) REVERT: B 87 GLN cc_start: 0.8179 (mt0) cc_final: 0.7968 (mm-40) REVERT: B 144 THR cc_start: 0.8715 (t) cc_final: 0.8457 (m) REVERT: G 87 GLN cc_start: 0.8013 (mt0) cc_final: 0.7731 (mm-40) outliers start: 31 outliers final: 24 residues processed: 126 average time/residue: 0.1651 time to fit residues: 29.1419 Evaluate side-chains 135 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN D 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7455 Z= 0.395 Angle : 0.612 8.077 10199 Z= 0.305 Chirality : 0.049 0.159 1302 Planarity : 0.004 0.031 1295 Dihedral : 5.364 45.263 1057 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 4.27 % Allowed : 16.24 % Favored : 79.49 % 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: 0.70 (0.24), residues: 1008 helix: -5.04 (0.27), residues: 42 sheet: 1.68 (0.25), residues: 364 loop : 0.17 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 84 HIS 0.003 0.001 HIS F 50 PHE 0.007 0.001 PHE C 40 TYR 0.013 0.002 TYR A 33 ARG 0.001 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 0.868 Fit side-chains REVERT: A 56 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8232 (mttt) REVERT: A 87 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7879 (mm110) REVERT: C 21 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8030 (p0) REVERT: C 87 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7091 (mm-40) REVERT: D 56 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8527 (mtpt) REVERT: B 21 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7952 (p0) REVERT: B 53 ASP cc_start: 0.8146 (t0) cc_final: 0.7896 (t0) REVERT: B 87 GLN cc_start: 0.8218 (mt0) cc_final: 0.7991 (mm-40) REVERT: B 144 THR cc_start: 0.8727 (t) cc_final: 0.8426 (m) REVERT: G 87 GLN cc_start: 0.8026 (mt0) cc_final: 0.7732 (mm-40) outliers start: 35 outliers final: 28 residues processed: 126 average time/residue: 0.1607 time to fit residues: 28.4787 Evaluate side-chains 137 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0030 chunk 88 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN G 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7455 Z= 0.112 Angle : 0.423 4.359 10199 Z= 0.216 Chirality : 0.043 0.145 1302 Planarity : 0.003 0.032 1295 Dihedral : 4.292 36.526 1057 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.81 % Allowed : 17.83 % Favored : 79.37 % 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: 1.14 (0.25), residues: 1008 helix: -4.64 (0.34), residues: 42 sheet: 2.04 (0.26), residues: 364 loop : 0.40 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.003 0.001 PHE G 40 TYR 0.005 0.001 TYR G 33 ARG 0.001 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.922 Fit side-chains REVERT: A 56 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8152 (mttt) REVERT: A 67 GLN cc_start: 0.8552 (mt0) cc_final: 0.8103 (mt0) REVERT: A 87 GLN cc_start: 0.8048 (mt0) cc_final: 0.7782 (mm110) REVERT: D 56 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8527 (mtpt) REVERT: E 83 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8609 (m) REVERT: B 21 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7637 (p0) REVERT: B 144 THR cc_start: 0.8782 (t) cc_final: 0.8527 (m) REVERT: G 87 GLN cc_start: 0.8029 (mt0) cc_final: 0.7772 (mm-40) outliers start: 23 outliers final: 18 residues processed: 121 average time/residue: 0.1640 time to fit residues: 27.8332 Evaluate side-chains 120 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.0030 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN D 23 ASN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7455 Z= 0.119 Angle : 0.430 5.117 10199 Z= 0.217 Chirality : 0.044 0.144 1302 Planarity : 0.003 0.030 1295 Dihedral : 4.075 31.226 1057 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.44 % Allowed : 18.19 % Favored : 79.37 % 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: 1.30 (0.25), residues: 1008 helix: -4.16 (0.45), residues: 42 sheet: 2.21 (0.26), residues: 364 loop : 0.45 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.004 0.001 PHE G 40 TYR 0.006 0.001 TYR A 33 ARG 0.001 0.000 ARG A 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.937 Fit side-chains REVERT: A 56 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8106 (mttt) REVERT: A 67 GLN cc_start: 0.8579 (mt0) cc_final: 0.8142 (mt0) REVERT: A 87 GLN cc_start: 0.8051 (mt0) cc_final: 0.7790 (mm110) REVERT: C 21 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7926 (p0) REVERT: C 143 MET cc_start: 0.8138 (ttm) cc_final: 0.7929 (ttm) REVERT: D 56 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8484 (mtpt) REVERT: G 87 GLN cc_start: 0.8037 (mt0) cc_final: 0.7780 (mm-40) outliers start: 20 outliers final: 17 residues processed: 113 average time/residue: 0.1768 time to fit residues: 27.8026 Evaluate side-chains 115 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 67 GLN D 23 ASN D 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.094126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.084025 restraints weight = 9239.984| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.30 r_work: 0.2669 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7455 Z= 0.160 Angle : 0.455 4.974 10199 Z= 0.229 Chirality : 0.044 0.146 1302 Planarity : 0.003 0.030 1295 Dihedral : 4.232 31.510 1057 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.69 % Allowed : 18.07 % Favored : 79.24 % 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: 1.31 (0.25), residues: 1008 helix: -3.92 (0.50), residues: 42 sheet: 2.21 (0.26), residues: 364 loop : 0.43 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.003 0.001 PHE C 40 TYR 0.008 0.001 TYR A 33 ARG 0.001 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.57 seconds wall clock time: 30 minutes 32.13 seconds (1832.13 seconds total)