Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 04:55:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shs_10204/08_2023/6shs_10204.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shs_10204/08_2023/6shs_10204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shs_10204/08_2023/6shs_10204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shs_10204/08_2023/6shs_10204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shs_10204/08_2023/6shs_10204.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6shs_10204/08_2023/6shs_10204.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 2328 2.51 5 N 636 2.21 5 O 684 1.98 5 H 3408 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 7068 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "B" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "C" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "H" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "D" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "I" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "E" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "J" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "F" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "K" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Chain: "L" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 589 Classifications: {'peptide': 40} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 39} Time building chain proxies: 3.41, per 1000 atoms: 0.48 Number of scatterers: 7068 At special positions: 0 Unit cell: (70.2, 98.55, 48.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 684 8.00 N 636 7.00 C 2328 6.00 H 3408 1.00 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: 5.52 Conformation dependent library (CDL) restraints added in 588.0 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 12 removed outlier: 7.103A pdb=" N TYR D 10 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU C 11 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL D 12 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR C 10 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU A 11 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL C 12 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA A 2 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ARG E 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE A 4 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASP E 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS A 6 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLY E 9 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N SER A 8 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU E 11 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N TYR A 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA E 2 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ARG F 5 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE E 4 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP F 7 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS E 6 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLY F 9 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N SER E 8 " --> pdb=" O GLY F 9 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU F 11 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N TYR E 10 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA F 2 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ARG G 5 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE F 4 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP G 7 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS F 6 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY G 9 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N SER F 8 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU G 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N TYR F 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.497A pdb=" N LYS A 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE E 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS E 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N PHE F 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS F 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE G 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL F 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 33 through 34 removed outlier: 6.754A pdb=" N GLY C 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 3 through 12 removed outlier: 6.098A pdb=" N GLU H 3 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N HIS I 6 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG H 5 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N SER I 8 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP H 7 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TYR I 10 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLY H 9 " --> pdb=" O TYR I 10 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N VAL I 12 " --> pdb=" O GLY H 9 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N GLU H 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU B 3 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N HIS H 6 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG B 5 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N SER H 8 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP B 7 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TYR H 10 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLY B 9 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N VAL H 12 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N GLU B 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 10 " --> pdb=" O GLY J 9 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLU J 11 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL B 12 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR J 10 " --> pdb=" O GLY K 9 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU K 11 " --> pdb=" O TYR J 10 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL J 12 " --> pdb=" O GLU K 11 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR K 10 " --> pdb=" O GLY L 9 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU L 11 " --> pdb=" O TYR K 10 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL K 12 " --> pdb=" O GLU L 11 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 15 through 19 removed outlier: 6.441A pdb=" N LYS B 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N PHE J 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS J 16 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N PHE K 19 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL J 18 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS K 16 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N PHE L 19 " --> pdb=" O LYS K 16 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL K 18 " --> pdb=" O PHE L 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 33 through 34 removed outlier: 6.806A pdb=" N GLY H 33 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY B 33 " --> pdb=" O LEU H 34 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 162 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: 1.97 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3408 1.03 - 1.22: 0 1.22 - 1.41: 1668 1.41 - 1.61: 2040 1.61 - 1.80: 24 Bond restraints: 7140 Sorted by residual: bond pdb=" CG1 ILE H 31 " pdb=" CD1 ILE H 31 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.20e+00 bond pdb=" CG1 ILE C 31 " pdb=" CD1 ILE C 31 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.18e+00 bond pdb=" CG1 ILE E 31 " pdb=" CD1 ILE E 31 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.18e+00 bond pdb=" CG1 ILE G 31 " pdb=" CD1 ILE G 31 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.18e+00 bond pdb=" CG1 ILE A 31 " pdb=" CD1 ILE A 31 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.17e+00 ... (remaining 7135 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.08: 25 106.08 - 112.37: 8090 112.37 - 118.65: 1371 118.65 - 124.93: 2985 124.93 - 131.22: 321 Bond angle restraints: 12792 Sorted by residual: angle pdb=" C HIS J 13 " pdb=" CA HIS J 13 " pdb=" CB HIS J 13 " ideal model delta sigma weight residual 111.95 107.01 4.94 2.38e+00 1.77e-01 4.31e+00 angle pdb=" C HIS C 13 " pdb=" CA HIS C 13 " pdb=" CB HIS C 13 " ideal model delta sigma weight residual 111.95 107.02 4.93 2.38e+00 1.77e-01 4.29e+00 angle pdb=" C HIS E 13 " pdb=" CA HIS E 13 " pdb=" CB HIS E 13 " ideal model delta sigma weight residual 111.95 107.03 4.92 2.38e+00 1.77e-01 4.27e+00 angle pdb=" C HIS L 13 " pdb=" CA HIS L 13 " pdb=" CB HIS L 13 " ideal model delta sigma weight residual 111.95 107.03 4.92 2.38e+00 1.77e-01 4.27e+00 angle pdb=" C HIS F 13 " pdb=" CA HIS F 13 " pdb=" CB HIS F 13 " ideal model delta sigma weight residual 111.95 107.04 4.91 2.38e+00 1.77e-01 4.26e+00 ... (remaining 12787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.57: 2100 8.57 - 17.14: 396 17.14 - 25.70: 222 25.70 - 34.27: 54 34.27 - 42.84: 60 Dihedral angle restraints: 2832 sinusoidal: 1188 harmonic: 1644 Sorted by residual: dihedral pdb=" CA HIS J 13 " pdb=" C HIS J 13 " pdb=" N HIS J 14 " pdb=" CA HIS J 14 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA HIS I 13 " pdb=" C HIS I 13 " pdb=" N HIS I 14 " pdb=" CA HIS I 14 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA HIS G 13 " pdb=" C HIS G 13 " pdb=" N HIS G 14 " pdb=" CA HIS G 14 " ideal model delta harmonic sigma weight residual 180.00 154.28 25.72 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 2829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 194 0.029 - 0.059: 89 0.059 - 0.088: 116 0.088 - 0.117: 105 0.117 - 0.146: 24 Chirality restraints: 528 Sorted by residual: chirality pdb=" CB ILE F 32 " pdb=" CA ILE F 32 " pdb=" CG1 ILE F 32 " pdb=" CG2 ILE F 32 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CB ILE C 32 " pdb=" CA ILE C 32 " pdb=" CG1 ILE C 32 " pdb=" CG2 ILE C 32 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CB ILE H 32 " pdb=" CA ILE H 32 " pdb=" CG1 ILE H 32 " pdb=" CG2 ILE H 32 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 17 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C LEU H 17 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU H 17 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL H 18 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 17 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C LEU E 17 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU E 17 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL E 18 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 17 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C LEU F 17 " -0.021 2.00e-02 2.50e+03 pdb=" O LEU F 17 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL F 18 " 0.007 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 1167 2.27 - 2.85: 14919 2.85 - 3.43: 16491 3.43 - 4.02: 23667 4.02 - 4.60: 34418 Nonbonded interactions: 90662 Sorted by model distance: nonbonded pdb=" OE1 GLU E 11 " pdb=" HZ1 LYS E 16 " model vdw 1.684 1.850 nonbonded pdb=" OE1 GLU C 11 " pdb=" HZ1 LYS C 16 " model vdw 1.684 1.850 nonbonded pdb=" OE1 GLU F 11 " pdb=" HZ1 LYS F 16 " model vdw 1.684 1.850 nonbonded pdb=" OE1 GLU K 11 " pdb=" HZ1 LYS K 16 " model vdw 1.684 1.850 nonbonded pdb=" OE1 GLU G 11 " pdb=" HZ1 LYS G 16 " model vdw 1.684 1.850 ... (remaining 90657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.120 Extract box with map and model: 1.380 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.410 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 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 : 0.009 0.058 3732 Z= 0.618 Angle : 1.019 4.938 5004 Z= 0.568 Chirality : 0.065 0.146 528 Planarity : 0.004 0.012 660 Dihedral : 12.042 39.868 1272 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.05 % Favored : 78.95 % 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: -5.87 (0.22), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.17), residues: 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4776 time to fit residues: 69.1757 Evaluate side-chains 68 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3732 Z= 0.278 Angle : 0.726 5.174 5004 Z= 0.390 Chirality : 0.055 0.159 528 Planarity : 0.005 0.055 660 Dihedral : 7.366 28.747 492 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.76 % Favored : 82.24 % 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: -5.46 (0.22), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.17), residues: 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3112 time to fit residues: 30.6332 Evaluate side-chains 55 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN H 27 ASN I 27 ASN J 27 ASN K 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.014 3732 Z= 0.157 Angle : 0.562 3.495 5004 Z= 0.309 Chirality : 0.052 0.146 528 Planarity : 0.002 0.018 660 Dihedral : 6.625 24.157 492 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % 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: -5.43 (0.22), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.16), residues: 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2988 time to fit residues: 27.6462 Evaluate side-chains 49 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 0.0030 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 3732 Z= 0.281 Angle : 0.643 4.126 5004 Z= 0.352 Chirality : 0.053 0.147 528 Planarity : 0.003 0.024 660 Dihedral : 6.856 25.803 492 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.08 % Favored : 80.92 % 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: -5.60 (0.21), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.26 (0.16), residues: 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2450 time to fit residues: 21.3006 Evaluate side-chains 41 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3732 Z= 0.144 Angle : 0.519 3.523 5004 Z= 0.287 Chirality : 0.052 0.154 528 Planarity : 0.002 0.011 660 Dihedral : 6.266 22.702 492 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.57 % Favored : 84.43 % 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: -5.41 (0.22), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.17), residues: 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2138 time to fit residues: 18.2804 Evaluate side-chains 40 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3732 Z= 0.143 Angle : 0.511 3.584 5004 Z= 0.282 Chirality : 0.052 0.153 528 Planarity : 0.002 0.011 660 Dihedral : 6.006 21.840 492 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % 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: -5.42 (0.23), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.17), residues: 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2404 time to fit residues: 20.5010 Evaluate side-chains 46 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 28 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.7051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 3732 Z= 0.189 Angle : 0.537 3.170 5004 Z= 0.296 Chirality : 0.053 0.149 528 Planarity : 0.002 0.011 660 Dihedral : 6.216 24.519 492 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.64 % Favored : 81.36 % 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: -5.46 (0.23), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.17), residues: 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2093 time to fit residues: 17.2943 Evaluate side-chains 43 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.7569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 3732 Z= 0.273 Angle : 0.605 3.885 5004 Z= 0.335 Chirality : 0.053 0.147 528 Planarity : 0.003 0.015 660 Dihedral : 6.615 25.906 492 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.27 % Favored : 78.73 % 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: -5.67 (0.22), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.17), residues: 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2341 time to fit residues: 16.7038 Evaluate side-chains 41 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.7796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3732 Z= 0.204 Angle : 0.558 3.376 5004 Z= 0.311 Chirality : 0.053 0.148 528 Planarity : 0.002 0.007 660 Dihedral : 6.412 24.870 492 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.64 % Favored : 81.36 % 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: -5.53 (0.23), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.17), residues: 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2255 time to fit residues: 17.0130 Evaluate side-chains 42 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.0370 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.0270 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN H 27 ASN I 27 ASN J 27 ASN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN K 27 ASN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.7913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 3732 Z= 0.127 Angle : 0.505 3.417 5004 Z= 0.281 Chirality : 0.052 0.153 528 Planarity : 0.001 0.007 660 Dihedral : 5.948 22.309 492 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % 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: -5.34 (0.23), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.18), residues: 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2098 time to fit residues: 15.7716 Evaluate side-chains 41 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.128373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.111959 restraints weight = 28126.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.115116 restraints weight = 17663.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.117622 restraints weight = 12294.057| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.7973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.013 3732 Z= 0.125 Angle : 0.485 3.319 5004 Z= 0.271 Chirality : 0.053 0.149 528 Planarity : 0.001 0.006 660 Dihedral : 5.768 21.968 492 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.45 % Favored : 83.55 % 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: -5.25 (0.24), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.18), residues: 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.90 seconds wall clock time: 45 minutes 47.01 seconds (2747.01 seconds total)