Starting phenix.real_space_refine (version: dev) on Sun Dec 11 22:58:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flt_4276/12_2022/6flt_4276.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flt_4276/12_2022/6flt_4276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flt_4276/12_2022/6flt_4276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flt_4276/12_2022/6flt_4276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flt_4276/12_2022/6flt_4276.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flt_4276/12_2022/6flt_4276.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8060 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "F" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "H" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "I" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Time building chain proxies: 4.08, per 1000 atoms: 0.51 Number of scatterers: 8060 At special positions: 0 Unit cell: (93.903, 88.917, 43.212, 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) O 800 8.00 N 680 7.00 C 2480 6.00 H 4100 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: 6.16 Conformation dependent library (CDL) restraints added in 627.0 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 980 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 59 removed outlier: 8.006A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N THR E 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N ALA E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N LYS E 58 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU C 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY E 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N THR G 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N ALA G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N VAL E 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N LYS G 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU E 57 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLY G 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 10.606A pdb=" N THR I 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N ALA I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N LYS I 58 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU G 57 " --> pdb=" O LYS I 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'B' and resid 50 through 59 removed outlier: 8.012A pdb=" N GLY B 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N THR D 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ALA B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N LYS D 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU B 57 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY D 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N THR F 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ALA D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N ALA F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N VAL D 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N LYS F 58 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU D 57 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLY F 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N THR H 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ALA F 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N ALA H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N VAL F 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 10.175A pdb=" N LYS H 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU F 57 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY H 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N THR J 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ALA H 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N ALA J 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N VAL H 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N LYS J 58 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU H 57 " --> pdb=" O LYS J 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'E' and resid 87 through 88 removed outlier: 7.026A pdb=" N SER E 87 " --> pdb=" O ILE G 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 78 through 79 removed outlier: 6.639A pdb=" N ALA G 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 8 hydrogen bonds defined for protein. 24 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: 2.45 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 0.98: 4088 0.98 - 1.12: 12 1.12 - 1.26: 690 1.26 - 1.40: 770 1.40 - 1.54: 2520 Bond restraints: 8080 Sorted by residual: bond pdb=" CA ALA A 78 " pdb=" CB ALA A 78 " ideal model delta sigma weight residual 1.536 1.457 0.079 2.08e-02 2.31e+03 1.43e+01 bond pdb=" CA ALA J 78 " pdb=" CB ALA J 78 " ideal model delta sigma weight residual 1.536 1.457 0.079 2.08e-02 2.31e+03 1.43e+01 bond pdb=" CA ALA F 78 " pdb=" CB ALA F 78 " ideal model delta sigma weight residual 1.536 1.457 0.078 2.08e-02 2.31e+03 1.42e+01 bond pdb=" CA ALA H 78 " pdb=" CB ALA H 78 " ideal model delta sigma weight residual 1.536 1.458 0.078 2.08e-02 2.31e+03 1.41e+01 bond pdb=" CA ALA B 78 " pdb=" CB ALA B 78 " ideal model delta sigma weight residual 1.536 1.458 0.078 2.08e-02 2.31e+03 1.41e+01 ... (remaining 8075 not shown) Histogram of bond angle deviations from ideal: 100.25 - 106.37: 230 106.37 - 112.50: 9788 112.50 - 118.62: 1739 118.62 - 124.75: 2745 124.75 - 130.87: 158 Bond angle restraints: 14660 Sorted by residual: angle pdb=" CA LEU F 38 " pdb=" CB LEU F 38 " pdb=" HB3 LEU F 38 " ideal model delta sigma weight residual 109.00 100.25 8.75 3.00e+00 1.11e-01 8.51e+00 angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" HB3 LEU C 38 " ideal model delta sigma weight residual 109.00 100.30 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" CA LEU G 38 " pdb=" CB LEU G 38 " pdb=" HB3 LEU G 38 " ideal model delta sigma weight residual 109.00 100.34 8.66 3.00e+00 1.11e-01 8.34e+00 angle pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" HB3 LEU B 38 " ideal model delta sigma weight residual 109.00 100.41 8.59 3.00e+00 1.11e-01 8.20e+00 angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" HB3 LEU A 38 " ideal model delta sigma weight residual 109.00 100.54 8.46 3.00e+00 1.11e-01 7.95e+00 ... (remaining 14655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.72: 2375 6.72 - 13.44: 431 13.44 - 20.16: 145 20.16 - 26.87: 91 26.87 - 33.59: 28 Dihedral angle restraints: 3070 sinusoidal: 1390 harmonic: 1680 Sorted by residual: dihedral pdb=" CA LEU B 38 " pdb=" C LEU B 38 " pdb=" N TYR B 39 " pdb=" CA TYR B 39 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA LEU H 38 " pdb=" C LEU H 38 " pdb=" N TYR H 39 " pdb=" CA TYR H 39 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA LEU E 38 " pdb=" C LEU E 38 " pdb=" N TYR E 39 " pdb=" CA TYR E 39 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 3067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 372 0.037 - 0.073: 158 0.073 - 0.110: 101 0.110 - 0.146: 79 0.146 - 0.183: 10 Chirality restraints: 720 Sorted by residual: chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CB VAL B 70 " pdb=" CA VAL B 70 " pdb=" CG1 VAL B 70 " pdb=" CG2 VAL B 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CB VAL H 70 " pdb=" CA VAL H 70 " pdb=" CG1 VAL H 70 " pdb=" CG2 VAL H 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.34e-01 ... (remaining 717 not shown) Planarity restraints: 1210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 94 " 0.009 2.00e-02 2.50e+03 1.01e-02 3.07e+00 pdb=" CG PHE I 94 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE I 94 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE I 94 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE I 94 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE I 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE I 94 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE I 94 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 PHE I 94 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE I 94 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE I 94 " 0.010 2.00e-02 2.50e+03 pdb=" HZ PHE I 94 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 94 " -0.009 2.00e-02 2.50e+03 9.45e-03 2.68e+00 pdb=" CG PHE J 94 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE J 94 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE J 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE J 94 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE J 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE J 94 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE J 94 " 0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE J 94 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE J 94 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE J 94 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE J 94 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.014 2.00e-02 2.50e+03 9.03e-03 2.45e+00 pdb=" CG PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE B 94 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 PHE B 94 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 PHE B 94 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 94 " 0.002 2.00e-02 2.50e+03 ... (remaining 1207 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.14: 274 2.14 - 2.73: 15252 2.73 - 3.32: 18961 3.32 - 3.91: 25539 3.91 - 4.50: 38419 Nonbonded interactions: 98445 Sorted by model distance: nonbonded pdb=" OE1 GLU E 46 " pdb=" HZ1 LYS G 80 " model vdw 1.554 1.850 nonbonded pdb=" OE1 GLU C 46 " pdb=" HZ1 LYS E 80 " model vdw 1.611 1.850 nonbonded pdb=" OE1 GLU D 46 " pdb=" HZ1 LYS F 80 " model vdw 1.624 1.850 nonbonded pdb=" OE1 GLU F 46 " pdb=" HZ1 LYS H 80 " model vdw 1.639 1.850 nonbonded pdb=" OE1 GLU A 46 " pdb=" HZ1 LYS C 80 " model vdw 1.704 1.850 ... (remaining 98440 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 2480 2.51 5 N 680 2.21 5 O 800 1.98 5 H 4100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.130 Extract box with map and model: 5.140 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.060 Process input model: 28.190 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.014 0.079 3980 Z= 0.901 Angle : 1.153 4.465 5400 Z= 0.679 Chirality : 0.063 0.183 720 Planarity : 0.004 0.011 670 Dihedral : 8.306 29.725 1310 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % 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: -5.36 (0.20), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.15), residues: 560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1534 time to fit residues: 18.3203 Evaluate side-chains 61 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.595 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.0010 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 3980 Z= 0.146 Angle : 0.549 6.831 5400 Z= 0.307 Chirality : 0.048 0.122 720 Planarity : 0.001 0.007 670 Dihedral : 7.075 19.728 580 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.21), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.16), residues: 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.646 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.1686 time to fit residues: 16.4746 Evaluate side-chains 67 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0968 time to fit residues: 2.1685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.2980 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 3980 Z= 0.299 Angle : 0.664 5.341 5400 Z= 0.394 Chirality : 0.050 0.122 720 Planarity : 0.002 0.010 670 Dihedral : 7.628 22.059 580 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.04 % Favored : 81.96 % Rotamer Outliers : 7.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.24), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.18), residues: 560 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 49 time to evaluate : 0.571 Fit side-chains outliers start: 31 outliers final: 25 residues processed: 70 average time/residue: 0.1557 time to fit residues: 16.5606 Evaluate side-chains 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 46 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0989 time to fit residues: 4.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 3980 Z= 0.360 Angle : 0.688 4.566 5400 Z= 0.412 Chirality : 0.051 0.133 720 Planarity : 0.003 0.011 670 Dihedral : 7.906 23.807 580 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.82 % Favored : 80.18 % Rotamer Outliers : 5.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.24), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.18), residues: 560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 0.639 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 63 average time/residue: 0.1693 time to fit residues: 16.2055 Evaluate side-chains 55 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.642 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0943 time to fit residues: 3.1855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 3980 Z= 0.289 Angle : 0.620 5.247 5400 Z= 0.371 Chirality : 0.050 0.127 720 Planarity : 0.002 0.008 670 Dihedral : 7.528 23.203 580 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.39 % Favored : 81.61 % Rotamer Outliers : 4.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.23), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.18), residues: 560 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 43 time to evaluate : 0.634 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 58 average time/residue: 0.1789 time to fit residues: 15.8872 Evaluate side-chains 54 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1000 time to fit residues: 3.1965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 0.0570 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.8242 ------------------------------------------------------------------------------- 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: 0.7655 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 3980 Z= 0.214 Angle : 0.551 3.786 5400 Z= 0.329 Chirality : 0.049 0.123 720 Planarity : 0.002 0.006 670 Dihedral : 7.148 22.443 580 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.04 % Favored : 81.96 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.23), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.18), residues: 560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.619 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 0.1807 time to fit residues: 13.3457 Evaluate side-chains 46 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1010 time to fit residues: 2.4703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: 0.7693 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 3980 Z= 0.262 Angle : 0.584 3.870 5400 Z= 0.351 Chirality : 0.050 0.126 720 Planarity : 0.002 0.007 670 Dihedral : 7.165 22.196 580 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.82 % Favored : 80.18 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.23), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.18), residues: 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.631 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.1861 time to fit residues: 11.8978 Evaluate side-chains 41 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0963 time to fit residues: 1.7356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.014 3980 Z= 0.136 Angle : 0.482 3.259 5400 Z= 0.286 Chirality : 0.049 0.120 720 Planarity : 0.001 0.005 670 Dihedral : 6.530 21.040 580 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.24), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.18), residues: 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.659 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1786 time to fit residues: 10.4714 Evaluate side-chains 37 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0889 time to fit residues: 0.8373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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: 0.7685 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 3980 Z= 0.260 Angle : 0.569 3.651 5400 Z= 0.342 Chirality : 0.049 0.127 720 Planarity : 0.002 0.007 670 Dihedral : 6.849 20.919 580 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.46 % Favored : 80.54 % Rotamer Outliers : 1.00 % 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: -4.81 (0.24), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.18), residues: 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.614 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.1865 time to fit residues: 11.6509 Evaluate side-chains 40 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0973 time to fit residues: 1.2245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3980 Z= 0.272 Angle : 0.585 3.709 5400 Z= 0.350 Chirality : 0.050 0.126 720 Planarity : 0.002 0.007 670 Dihedral : 7.057 21.435 580 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.29 % Favored : 80.71 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.23), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.18), residues: 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.647 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1925 time to fit residues: 10.9269 Evaluate side-chains 36 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.211964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.189144 restraints weight = 14472.495| |-----------------------------------------------------------------------------| r_work (start): 0.4642 rms_B_bonded: 2.82 r_work: 0.4545 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3980 Z= 0.301 Angle : 0.609 3.871 5400 Z= 0.365 Chirality : 0.050 0.126 720 Planarity : 0.002 0.008 670 Dihedral : 7.171 22.368 580 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.71 % Favored : 79.29 % 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: -5.03 (0.24), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.18), residues: 560 =============================================================================== Job complete usr+sys time: 2356.86 seconds wall clock time: 42 minutes 28.95 seconds (2548.95 seconds total)