Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 10:23:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/08_2023/6peo_20328.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/08_2023/6peo_20328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/08_2023/6peo_20328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/08_2023/6peo_20328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/08_2023/6peo_20328.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6peo_20328/08_2023/6peo_20328.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 1.000 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: 3 Type Number sf(0) Gaussians C 1375 2.51 5 N 380 2.21 5 O 450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 98": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 2205 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "B" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "C" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "D" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "E" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Time building chain proxies: 1.54, per 1000 atoms: 0.70 Number of scatterers: 2205 At special positions: 0 Unit cell: (74.55, 60.705, 39.405, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 450 8.00 N 380 7.00 C 1375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 342.2 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 70.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.490A pdb=" N VAL A 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL C 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL E 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 66 removed outlier: 6.774A pdb=" N VAL D 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN D 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU B 61 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN D 62 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 63 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR D 64 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN B 65 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL D 66 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN B 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU A 61 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN B 62 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 63 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR B 64 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN A 65 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 66 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR A 44 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY C 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N GLU A 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL C 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N GLY C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN A 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA C 53 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL C 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLU C 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N THR C 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS A 58 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU C 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N VAL C 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLN A 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N ASN C 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR A 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR C 44 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY E 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLU C 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL E 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N GLY E 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN C 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA E 53 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL C 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL E 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLU E 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR E 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS C 58 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS C 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL E 63 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLN C 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ASN E 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N THR C 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.460A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 74 through 83 removed outlier: 6.964A pdb=" N THR B 81 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL D 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU B 83 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU A 83 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLN C 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N GLU C 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL A 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL E 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA C 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLN E 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N GLU E 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N VAL C 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 96 removed outlier: 8.242A pdb=" N ALA B 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR D 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ALA B 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N PHE D 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR B 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE B 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY A 93 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LYS B 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 95 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA C 91 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY C 93 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA E 91 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 92 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY E 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 0.53 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 395 1.29 - 1.36: 340 1.36 - 1.42: 75 1.42 - 1.49: 374 1.49 - 1.55: 1026 Bond restraints: 2210 Sorted by residual: bond pdb=" CA GLU B 57 " pdb=" CB GLU B 57 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.50e-02 4.44e+03 1.01e+00 bond pdb=" CA GLU E 57 " pdb=" CB GLU E 57 " ideal model delta sigma weight residual 1.530 1.516 0.015 1.50e-02 4.44e+03 9.49e-01 bond pdb=" CA GLU D 57 " pdb=" CB GLU D 57 " ideal model delta sigma weight residual 1.530 1.516 0.015 1.50e-02 4.44e+03 9.36e-01 bond pdb=" CA GLU A 57 " pdb=" CB GLU A 57 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.50e-02 4.44e+03 9.19e-01 bond pdb=" CA GLU C 57 " pdb=" CB GLU C 57 " ideal model delta sigma weight residual 1.530 1.517 0.014 1.50e-02 4.44e+03 8.56e-01 ... (remaining 2205 not shown) Histogram of bond angle deviations from ideal: 106.29 - 109.75: 308 109.75 - 113.21: 1048 113.21 - 116.67: 386 116.67 - 120.13: 229 120.13 - 123.59: 1014 Bond angle restraints: 2985 Sorted by residual: angle pdb=" N GLU B 61 " pdb=" CA GLU B 61 " pdb=" CB GLU B 61 " ideal model delta sigma weight residual 110.69 113.10 -2.41 1.61e+00 3.86e-01 2.25e+00 angle pdb=" N GLU A 61 " pdb=" CA GLU A 61 " pdb=" CB GLU A 61 " ideal model delta sigma weight residual 110.69 113.08 -2.39 1.61e+00 3.86e-01 2.21e+00 angle pdb=" N GLU C 61 " pdb=" CA GLU C 61 " pdb=" CB GLU C 61 " ideal model delta sigma weight residual 110.69 113.08 -2.39 1.61e+00 3.86e-01 2.20e+00 angle pdb=" N GLU E 61 " pdb=" CA GLU E 61 " pdb=" CB GLU E 61 " ideal model delta sigma weight residual 110.69 113.07 -2.38 1.61e+00 3.86e-01 2.19e+00 angle pdb=" N GLU D 61 " pdb=" CA GLU D 61 " pdb=" CB GLU D 61 " ideal model delta sigma weight residual 110.69 113.07 -2.38 1.61e+00 3.86e-01 2.18e+00 ... (remaining 2980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.41: 1168 13.41 - 26.82: 97 26.82 - 40.23: 10 40.23 - 53.64: 20 53.64 - 67.05: 5 Dihedral angle restraints: 1300 sinusoidal: 440 harmonic: 860 Sorted by residual: dihedral pdb=" CA LYS A 60 " pdb=" C LYS A 60 " pdb=" N GLU A 61 " pdb=" CA GLU A 61 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LYS C 60 " pdb=" C LYS C 60 " pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LYS E 60 " pdb=" C LYS E 60 " pdb=" N GLU E 61 " pdb=" CA GLU E 61 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 1297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 188 0.027 - 0.054: 100 0.054 - 0.082: 30 0.082 - 0.109: 48 0.109 - 0.136: 24 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 387 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 60 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C LYS B 60 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS B 60 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU B 61 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 60 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C LYS A 60 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS A 60 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU A 61 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 60 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C LYS C 60 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS C 60 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU C 61 " -0.023 2.00e-02 2.50e+03 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1220 2.97 - 3.46: 1883 3.46 - 3.94: 3420 3.94 - 4.42: 3801 4.42 - 4.90: 7503 Nonbonded interactions: 17827 Sorted by model distance: nonbonded pdb=" NZ LYS B 58 " pdb=" OE1 GLU B 61 " model vdw 2.492 2.520 nonbonded pdb=" NZ LYS E 58 " pdb=" OE1 GLU E 61 " model vdw 2.492 2.520 nonbonded pdb=" NZ LYS D 58 " pdb=" OE1 GLU D 61 " model vdw 2.492 2.520 nonbonded pdb=" NZ LYS C 58 " pdb=" OE1 GLU C 61 " model vdw 2.492 2.520 nonbonded pdb=" NZ LYS A 58 " pdb=" OE1 GLU A 61 " model vdw 2.492 2.520 ... (remaining 17822 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.380 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 2210 Z= 0.198 Angle : 0.543 3.112 2985 Z= 0.309 Chirality : 0.054 0.136 390 Planarity : 0.007 0.040 375 Dihedral : 13.058 67.049 760 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.42), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.32), residues: 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1654 time to fit residues: 9.1518 Evaluate side-chains 34 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 overall best weight: 7.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.028 2210 Z= 0.440 Angle : 0.572 3.610 2985 Z= 0.328 Chirality : 0.058 0.137 390 Planarity : 0.002 0.014 375 Dihedral : 5.024 14.464 320 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.40), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.31), residues: 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.243 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.1659 time to fit residues: 8.6721 Evaluate side-chains 40 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0245 time to fit residues: 0.4905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 2210 Z= 0.185 Angle : 0.450 3.262 2985 Z= 0.255 Chirality : 0.053 0.126 390 Planarity : 0.002 0.012 375 Dihedral : 4.505 12.479 320 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.40), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.31), residues: 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.242 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.1646 time to fit residues: 8.2729 Evaluate side-chains 39 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0329 time to fit residues: 0.4911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.025 2210 Z= 0.389 Angle : 0.536 3.509 2985 Z= 0.305 Chirality : 0.057 0.132 390 Planarity : 0.002 0.012 375 Dihedral : 4.675 13.097 320 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer Outliers : 4.89 % 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: -2.01 (0.38), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.29), residues: 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.246 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 39 average time/residue: 0.1548 time to fit residues: 7.2385 Evaluate side-chains 37 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0469 time to fit residues: 0.6921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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: 0.7933 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 2210 Z= 0.273 Angle : 0.486 3.653 2985 Z= 0.277 Chirality : 0.054 0.129 390 Planarity : 0.002 0.013 375 Dihedral : 4.435 13.439 320 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 4.00 % 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: -2.10 (0.38), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.29), residues: 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.255 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 43 average time/residue: 0.1499 time to fit residues: 7.6200 Evaluate side-chains 36 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0348 time to fit residues: 0.4856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.7960 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.026 2210 Z= 0.379 Angle : 0.536 4.208 2985 Z= 0.303 Chirality : 0.055 0.135 390 Planarity : 0.002 0.010 375 Dihedral : 4.618 14.028 320 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer Outliers : 3.11 % 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: -2.27 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.29), residues: 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.201 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 34 average time/residue: 0.1400 time to fit residues: 5.6968 Evaluate side-chains 34 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0283 time to fit residues: 0.4823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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: 0.7939 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 2210 Z= 0.290 Angle : 0.503 4.527 2985 Z= 0.284 Chirality : 0.054 0.135 390 Planarity : 0.002 0.010 375 Dihedral : 4.454 13.787 320 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.89 % 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: -2.29 (0.38), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.29), residues: 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.252 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.1481 time to fit residues: 5.8179 Evaluate side-chains 33 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.199 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0332 time to fit residues: 0.3670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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: 0.7949 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.026 2210 Z= 0.323 Angle : 0.510 4.108 2985 Z= 0.289 Chirality : 0.055 0.136 390 Planarity : 0.002 0.009 375 Dihedral : 4.483 14.168 320 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer Outliers : 0.89 % 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: -2.39 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.227 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.1646 time to fit residues: 6.2592 Evaluate side-chains 32 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.249 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0281 time to fit residues: 0.3777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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: 0.7977 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.028 2210 Z= 0.442 Angle : 0.560 4.460 2985 Z= 0.318 Chirality : 0.057 0.138 390 Planarity : 0.002 0.009 375 Dihedral : 4.674 14.704 320 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer Outliers : 0.89 % 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: -2.51 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.28), residues: 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.243 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.1804 time to fit residues: 6.3515 Evaluate side-chains 32 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.244 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0376 time to fit residues: 0.4408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.2980 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- 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: 0.7945 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 2210 Z= 0.302 Angle : 0.534 5.813 2985 Z= 0.299 Chirality : 0.055 0.136 390 Planarity : 0.002 0.009 375 Dihedral : 4.449 14.064 320 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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: -2.48 (0.38), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.29), residues: 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.240 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1744 time to fit residues: 6.1646 Evaluate side-chains 30 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.240 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.129408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.111859 restraints weight = 2704.207| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.80 r_work: 0.3840 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.033 2210 Z= 0.404 Angle : 0.567 5.529 2985 Z= 0.319 Chirality : 0.056 0.136 390 Planarity : 0.002 0.009 375 Dihedral : 4.575 14.466 320 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer Outliers : 0.89 % 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: -2.54 (0.38), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.29), residues: 310 =============================================================================== Job complete usr+sys time: 773.33 seconds wall clock time: 14 minutes 45.79 seconds (885.79 seconds total)