Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 06:28:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/08_2023/8ehr_28150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/08_2023/8ehr_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_28150/08_2023/8ehr_28150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/08_2023/8ehr_28150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/08_2023/8ehr_28150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehr_28150/08_2023/8ehr_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-1.21rc1-5044/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: 4.36, per 1000 atoms: 0.59 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: 2.75 Conformation dependent library (CDL) restraints added in 1.1 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: 0.89 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: 1.98 Time building geometry restraints manager: 3.00 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: 0.420 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: 2.530 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.650 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.980 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.741 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1896 time to fit residues: 38.1261 Evaluate side-chains 102 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0895 ------------------------------------------------------------------------------- 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: 9.9990 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 48 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 7455 Z= 0.324 Angle : 0.588 7.636 10199 Z= 0.298 Chirality : 0.048 0.166 1302 Planarity : 0.004 0.030 1295 Dihedral : 5.150 35.448 1057 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer Outliers : 2.44 % 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: 1.10 (0.25), residues: 1008 helix: -5.30 (0.15), residues: 42 sheet: 1.83 (0.25), residues: 364 loop : 0.58 (0.23), residues: 602 *********************** 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 128 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.852 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.1930 time to fit residues: 32.7537 Evaluate side-chains 115 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0674 time to fit residues: 3.0444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN D 23 ASN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 ASN B 19 GLN F 23 ASN G 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 7455 Z= 0.174 Angle : 0.468 5.622 10199 Z= 0.238 Chirality : 0.045 0.154 1302 Planarity : 0.003 0.026 1295 Dihedral : 4.671 33.336 1057 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer Outliers : 1.22 % 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: 1.23 (0.25), residues: 1008 helix: -5.11 (0.20), residues: 42 sheet: 1.95 (0.25), residues: 364 loop : 0.64 (0.24), residues: 602 *********************** 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 127 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.766 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 125 average time/residue: 0.1710 time to fit residues: 29.8985 Evaluate side-chains 111 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0654 time to fit residues: 1.7767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN C 19 GLN C 67 GLN D 23 ASN B 19 GLN F 23 ASN G 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.049 7455 Z= 0.520 Angle : 0.699 9.776 10199 Z= 0.347 Chirality : 0.053 0.167 1302 Planarity : 0.004 0.030 1295 Dihedral : 5.763 46.977 1057 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 2.81 % 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: 0.67 (0.24), residues: 1008 helix: -5.25 (0.19), residues: 42 sheet: 1.57 (0.25), residues: 364 loop : 0.22 (0.22), residues: 602 *********************** 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 127 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.850 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 0.1804 time to fit residues: 29.2348 Evaluate side-chains 119 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0672 time to fit residues: 3.2268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 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 19 GLN C 67 GLN D 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2538 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= 0.243 Angle : 0.518 6.478 10199 Z= 0.261 Chirality : 0.046 0.153 1302 Planarity : 0.003 0.029 1295 Dihedral : 5.173 43.153 1057 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 1.22 % 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: 0.84 (0.24), residues: 1008 helix: -5.14 (0.24), residues: 42 sheet: 1.71 (0.25), residues: 364 loop : 0.32 (0.23), residues: 602 *********************** 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 114 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.729 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 112 average time/residue: 0.1635 time to fit residues: 25.7424 Evaluate side-chains 102 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0621 time to fit residues: 1.3085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN C 19 GLN C 67 GLN D 23 ASN D 50 HIS B 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.044 7455 Z= 0.463 Angle : 0.663 9.389 10199 Z= 0.329 Chirality : 0.051 0.162 1302 Planarity : 0.004 0.032 1295 Dihedral : 5.732 48.251 1057 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 1.95 % 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: 0.50 (0.24), residues: 1008 helix: -5.18 (0.25), residues: 42 sheet: 1.51 (0.26), residues: 364 loop : 0.05 (0.22), residues: 602 *********************** 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 116 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.869 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 108 average time/residue: 0.1822 time to fit residues: 27.2841 Evaluate side-chains 113 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0925 time to fit residues: 3.0534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 19 GLN C 67 GLN D 19 GLN D 23 ASN D 134 ASN B 23 ASN ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2643 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= 0.135 Angle : 0.454 4.377 10199 Z= 0.231 Chirality : 0.044 0.148 1302 Planarity : 0.003 0.030 1295 Dihedral : 4.733 41.563 1057 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 0.49 % 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: 0.90 (0.25), residues: 1008 helix: -4.99 (0.30), residues: 42 sheet: 1.85 (0.26), residues: 364 loop : 0.28 (0.23), residues: 602 *********************** 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 111 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.885 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 109 average time/residue: 0.1839 time to fit residues: 27.8360 Evaluate side-chains 104 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0674 time to fit residues: 1.4382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 0.0470 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- 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 19 GLN D 23 ASN E 77 GLN G 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 7455 Z= 0.360 Angle : 0.588 7.793 10199 Z= 0.294 Chirality : 0.049 0.156 1302 Planarity : 0.004 0.031 1295 Dihedral : 5.356 44.006 1057 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 0.37 % 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: 0.68 (0.24), residues: 1008 helix: -5.08 (0.28), residues: 42 sheet: 1.72 (0.26), residues: 364 loop : 0.11 (0.22), residues: 602 *********************** 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 103 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.755 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 101 average time/residue: 0.1800 time to fit residues: 25.2916 Evaluate side-chains 103 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0888 time to fit residues: 1.6030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.2980 chunk 88 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 52 ASN C 67 GLN D 19 GLN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN B 23 ASN G 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2726 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= 0.114 Angle : 0.431 4.683 10199 Z= 0.220 Chirality : 0.044 0.146 1302 Planarity : 0.003 0.032 1295 Dihedral : 4.417 37.609 1057 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 0.24 % 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: 1.05 (0.25), residues: 1008 helix: -4.81 (0.32), residues: 42 sheet: 2.05 (0.26), residues: 364 loop : 0.31 (0.23), residues: 602 *********************** 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 102 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.898 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.1814 time to fit residues: 25.5774 Evaluate side-chains 97 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0955 time to fit residues: 1.2668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 52 ASN C 67 GLN E 77 GLN B 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2750 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= 0.198 Angle : 0.487 5.303 10199 Z= 0.245 Chirality : 0.045 0.150 1302 Planarity : 0.003 0.030 1295 Dihedral : 4.625 37.823 1057 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer Outliers : 0.12 % 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: 1.05 (0.25), residues: 1008 helix: -4.63 (0.34), residues: 42 sheet: 1.63 (0.26), residues: 406 loop : 0.51 (0.24), residues: 560 ********************** 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 98 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.840 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1830 time to fit residues: 24.8364 Evaluate side-chains 97 residues out of total 819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0030 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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 52 ASN C 67 GLN D 23 ASN ** E 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.096602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.086705 restraints weight = 9178.973| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.24 r_work: 0.2700 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2781 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= 0.124 Angle : 0.426 4.678 10199 Z= 0.216 Chirality : 0.044 0.146 1302 Planarity : 0.003 0.030 1295 Dihedral : 4.112 33.293 1057 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer Outliers : 0.37 % 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: 1.26 (0.25), residues: 1008 helix: -4.23 (0.43), residues: 42 sheet: 2.24 (0.26), residues: 364 loop : 0.38 (0.24), residues: 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1586.33 seconds wall clock time: 29 minutes 45.75 seconds (1785.75 seconds total)