Starting phenix.real_space_refine (version: dev) on Sat May 14 17:46:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/05_2022/7k5y_22684.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/05_2022/7k5y_22684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/05_2022/7k5y_22684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/05_2022/7k5y_22684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/05_2022/7k5y_22684.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/05_2022/7k5y_22684.pdb" } resolution = 2.76 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= 0.105 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 None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 18258 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4015 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "J" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4062 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 10.47, per 1000 atoms: 0.57 Number of scatterers: 18258 At special positions: 0 Unit cell: (133.056, 121.968, 197.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 394 15.00 O 4252 8.00 N 3340 7.00 C 10240 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: 8.60 Conformation dependent library (CDL) restraints added in 1.8 seconds 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 23 sheets defined 49.0% alpha, 20.8% beta 194 base pairs and 357 stacking pairs defined. Time for finding SS restraints: 7.91 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.801A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.826A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.764A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.353A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.604A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.321A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.516A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.600A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.737A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 69 Processing helix chain 'U' and resid 71 through 74 removed outlier: 3.639A pdb=" N LYS U 74 " --> pdb=" O ASP U 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 71 through 74' Processing helix chain 'U' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.726A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.112A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.587A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.601A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.999A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.753A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.213A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.213A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.208A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N TYR M 181 " --> pdb=" O TYR M 201 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR M 201 " --> pdb=" O TYR M 181 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.208A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 removed outlier: 3.778A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.808A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.602A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.859A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 56 through 57 612 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 504 hydrogen bonds 1008 hydrogen bond angles 0 basepair planarities 194 basepair parallelities 357 stacking parallelities Total time for adding SS restraints: 7.44 Time building geometry restraints manager: 9.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3473 1.33 - 1.45: 6143 1.45 - 1.57: 8954 1.57 - 1.69: 786 1.69 - 1.81: 52 Bond restraints: 19408 Sorted by residual: bond pdb=" N SER M 26 " pdb=" CA SER M 26 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.50e+01 bond pdb=" C SER M 26 " pdb=" O SER M 26 " ideal model delta sigma weight residual 1.244 1.260 -0.016 9.10e-03 1.21e+04 3.15e+00 bond pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.68e+00 bond pdb=" CA SER M 26 " pdb=" C SER M 26 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.08e-02 8.57e+03 2.14e+00 bond pdb=" C3' DG I 153 " pdb=" O3' DG I 153 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.59e+00 ... (remaining 19403 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.05: 1737 105.05 - 112.29: 10727 112.29 - 119.53: 5900 119.53 - 126.78: 8402 126.78 - 134.02: 1149 Bond angle restraints: 27915 Sorted by residual: angle pdb=" CA SER M 26 " pdb=" C SER M 26 " pdb=" N PRO M 27 " ideal model delta sigma weight residual 120.58 122.54 -1.96 7.40e-01 1.83e+00 6.99e+00 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 113.18 119.19 -6.01 2.37e+00 1.78e-01 6.42e+00 angle pdb=" C3' DG J 128 " pdb=" C2' DG J 128 " pdb=" C1' DG J 128 " ideal model delta sigma weight residual 101.60 97.81 3.79 1.50e+00 4.44e-01 6.39e+00 angle pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sigma weight residual 120.20 123.94 -3.74 1.50e+00 4.44e-01 6.20e+00 angle pdb=" N SER N 50 " pdb=" CA SER N 50 " pdb=" CB SER N 50 " ideal model delta sigma weight residual 113.65 110.00 3.65 1.47e+00 4.63e-01 6.16e+00 ... (remaining 27910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 8254 34.24 - 68.47: 1996 68.47 - 102.71: 22 102.71 - 136.95: 3 136.95 - 171.18: 2 Dihedral angle restraints: 10277 sinusoidal: 6522 harmonic: 3755 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DT J 153 " pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sinusoidal sigma weight residual 220.00 48.82 171.18 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 119 " pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " pdb=" P DG J 120 " ideal model delta sinusoidal sigma weight residual 220.00 51.89 168.11 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 10274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2308 0.038 - 0.076: 668 0.076 - 0.113: 147 0.113 - 0.151: 27 0.151 - 0.189: 2 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CG LEU M 252 " pdb=" CB LEU M 252 " pdb=" CD1 LEU M 252 " pdb=" CD2 LEU M 252 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB THR M 177 " pdb=" CA THR M 177 " pdb=" OG1 THR M 177 " pdb=" CG2 THR M 177 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU N 252 " pdb=" CB LEU N 252 " pdb=" CD1 LEU N 252 " pdb=" CD2 LEU N 252 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 3149 not shown) Planarity restraints: 2154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY M 157 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO M 158 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO D 103 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 45 " 0.021 2.00e-02 2.50e+03 1.02e-02 2.86e+00 pdb=" N9 DA I 45 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 45 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 45 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 45 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 45 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 45 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA I 45 " -0.002 2.00e-02 2.50e+03 ... (remaining 2151 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 491 2.67 - 3.22: 15344 3.22 - 3.78: 33372 3.78 - 4.34: 45180 4.34 - 4.90: 64961 Nonbonded interactions: 159348 Sorted by model distance: nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG N 251 " model vdw 2.108 2.520 nonbonded pdb=" O SER N 156 " pdb=" OG1 THR N 263 " model vdw 2.171 2.440 nonbonded pdb=" OD2 ASP U 71 " pdb=" NZ LYS U 74 " model vdw 2.224 2.520 nonbonded pdb=" OG SER H 56 " pdb=" OP2 DA I 45 " model vdw 2.258 2.440 nonbonded pdb=" O GLN N 155 " pdb=" NE2 GLN N 261 " model vdw 2.275 2.520 ... (remaining 159343 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 5 Type Number sf(0) Gaussians P 394 5.49 5 S 32 5.16 5 C 10240 2.51 5 N 3340 2.21 5 O 4252 1.98 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 8.350 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.150 Process input model: 56.720 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.004 0.049 19408 Z= 0.242 Angle : 0.647 6.616 27915 Z= 0.397 Chirality : 0.038 0.189 3152 Planarity : 0.004 0.058 2154 Dihedral : 27.128 171.183 7871 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 1.74 (0.23), residues: 1271 helix: 2.37 (0.21), residues: 584 sheet: 0.64 (0.33), residues: 252 loop : -0.19 (0.28), residues: 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.475 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 1.6996 time to fit residues: 499.6099 Evaluate side-chains 204 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN M 25 GLN U 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 19408 Z= 0.302 Angle : 0.611 6.798 27915 Z= 0.360 Chirality : 0.038 0.167 3152 Planarity : 0.004 0.044 2154 Dihedral : 31.099 167.873 5387 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.28 % 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: 1.95 (0.24), residues: 1271 helix: 2.57 (0.21), residues: 586 sheet: 0.83 (0.33), residues: 262 loop : -0.21 (0.29), residues: 423 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 1.487 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 221 average time/residue: 1.6838 time to fit residues: 406.9784 Evaluate side-chains 198 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 1.623 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.8938 time to fit residues: 5.9605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 130 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 93 GLN G 24 GLN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 19408 Z= 0.324 Angle : 0.596 7.178 27915 Z= 0.351 Chirality : 0.037 0.145 3152 Planarity : 0.005 0.054 2154 Dihedral : 30.748 175.331 5387 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 3.20 % 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: 1.90 (0.24), residues: 1271 helix: 2.56 (0.21), residues: 586 sheet: 0.81 (0.33), residues: 262 loop : -0.30 (0.28), residues: 423 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 1.500 Fit side-chains outliers start: 35 outliers final: 18 residues processed: 212 average time/residue: 1.6070 time to fit residues: 374.3083 Evaluate side-chains 202 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.8178 time to fit residues: 9.6037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 19408 Z= 0.370 Angle : 0.601 7.222 27915 Z= 0.353 Chirality : 0.038 0.151 3152 Planarity : 0.005 0.047 2154 Dihedral : 30.761 172.806 5387 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 3.47 % 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: 1.73 (0.23), residues: 1271 helix: 2.40 (0.21), residues: 586 sheet: 0.77 (0.33), residues: 262 loop : -0.40 (0.28), residues: 423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 1.554 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 213 average time/residue: 1.6341 time to fit residues: 381.2111 Evaluate side-chains 204 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.9072 time to fit residues: 9.1318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 47 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 19408 Z= 0.272 Angle : 0.571 6.904 27915 Z= 0.340 Chirality : 0.036 0.173 3152 Planarity : 0.004 0.053 2154 Dihedral : 30.710 173.891 5387 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 2.65 % 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: 1.84 (0.23), residues: 1271 helix: 2.50 (0.21), residues: 586 sheet: 0.75 (0.33), residues: 262 loop : -0.30 (0.28), residues: 423 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 1.383 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 207 average time/residue: 1.6041 time to fit residues: 363.9833 Evaluate side-chains 206 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 12 residues processed: 9 average time/residue: 0.7301 time to fit residues: 9.7282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN M 154 GLN ** M 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 19408 Z= 0.370 Angle : 0.599 7.225 27915 Z= 0.352 Chirality : 0.038 0.167 3152 Planarity : 0.004 0.046 2154 Dihedral : 30.564 175.940 5387 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 2.92 % 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: 1.70 (0.23), residues: 1271 helix: 2.39 (0.21), residues: 586 sheet: 0.70 (0.33), residues: 262 loop : -0.38 (0.28), residues: 423 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.650 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 210 average time/residue: 1.6822 time to fit residues: 388.0550 Evaluate side-chains 207 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.7387 time to fit residues: 8.0497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN N 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 19408 Z= 0.262 Angle : 0.561 6.904 27915 Z= 0.333 Chirality : 0.035 0.161 3152 Planarity : 0.004 0.048 2154 Dihedral : 30.474 175.585 5387 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 2.83 % 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: 1.85 (0.24), residues: 1271 helix: 2.50 (0.21), residues: 592 sheet: 0.65 (0.33), residues: 262 loop : -0.25 (0.29), residues: 417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 1.614 Fit side-chains outliers start: 31 outliers final: 20 residues processed: 209 average time/residue: 1.6001 time to fit residues: 368.2186 Evaluate side-chains 206 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.8519 time to fit residues: 7.9673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN N 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 19408 Z= 0.319 Angle : 0.577 7.473 27915 Z= 0.341 Chirality : 0.037 0.156 3152 Planarity : 0.004 0.047 2154 Dihedral : 30.415 175.177 5387 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 2.28 % 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: 1.74 (0.24), residues: 1271 helix: 2.46 (0.21), residues: 586 sheet: 0.59 (0.33), residues: 262 loop : -0.32 (0.29), residues: 423 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.488 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 208 average time/residue: 1.6071 time to fit residues: 366.8526 Evaluate side-chains 206 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.5400 time to fit residues: 4.5306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN H 63 ASN N 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 19408 Z= 0.211 Angle : 0.561 6.877 27915 Z= 0.333 Chirality : 0.035 0.158 3152 Planarity : 0.004 0.046 2154 Dihedral : 30.423 175.366 5387 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.74 % 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: 1.87 (0.24), residues: 1271 helix: 2.54 (0.21), residues: 592 sheet: 0.60 (0.33), residues: 262 loop : -0.22 (0.29), residues: 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 1.419 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 205 average time/residue: 1.6381 time to fit residues: 368.9533 Evaluate side-chains 203 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 1.693 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 1.2504 time to fit residues: 4.6131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN N 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 19408 Z= 0.319 Angle : 0.580 7.091 27915 Z= 0.341 Chirality : 0.037 0.158 3152 Planarity : 0.004 0.050 2154 Dihedral : 30.366 175.833 5387 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.55 % 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: 1.76 (0.24), residues: 1271 helix: 2.43 (0.21), residues: 592 sheet: 0.61 (0.33), residues: 262 loop : -0.29 (0.29), residues: 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.507 Fit side-chains outliers start: 17 outliers final: 16 residues processed: 208 average time/residue: 1.5205 time to fit residues: 347.7762 Evaluate side-chains 206 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.6927 time to fit residues: 4.0871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 112 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 63 ASN M 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.171222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127837 restraints weight = 22853.850| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.21 r_work: 0.3707 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 1.11 restraints_weight: 0.2500 r_work: 0.3691 rms_B_bonded: 1.16 restraints_weight: 0.1250 r_work: 0.3682 rms_B_bonded: 1.23 restraints_weight: 0.0625 r_work: 0.3673 rms_B_bonded: 1.32 restraints_weight: 0.0312 r_work: 0.3664 rms_B_bonded: 1.43 restraints_weight: 0.0156 r_work: 0.3654 rms_B_bonded: 1.56 restraints_weight: 0.0078 r_work: 0.3644 rms_B_bonded: 1.70 restraints_weight: 0.0039 r_work: 0.3633 rms_B_bonded: 1.87 restraints_weight: 0.0020 r_work: 0.3621 rms_B_bonded: 2.05 restraints_weight: 0.0010 r_work: 0.3609 rms_B_bonded: 2.25 restraints_weight: 0.0005 r_work: 0.3596 rms_B_bonded: 2.47 restraints_weight: 0.0002 r_work: 0.3582 rms_B_bonded: 2.71 restraints_weight: 0.0001 r_work: 0.3568 rms_B_bonded: 2.97 restraints_weight: 0.0001 r_work: 0.3552 rms_B_bonded: 3.26 restraints_weight: 0.0000 r_work: 0.3534 rms_B_bonded: 3.58 restraints_weight: 0.0000 r_work: 0.3516 rms_B_bonded: 3.93 restraints_weight: 0.0000 r_work: 0.3496 rms_B_bonded: 4.31 restraints_weight: 0.0000 r_work: 0.3475 rms_B_bonded: 4.72 restraints_weight: 0.0000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 19408 Z= 0.204 Angle : 0.566 6.830 27915 Z= 0.336 Chirality : 0.035 0.155 3152 Planarity : 0.004 0.057 2154 Dihedral : 30.374 175.714 5387 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.55 % 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: 1.86 (0.24), residues: 1271 helix: 2.50 (0.21), residues: 592 sheet: 0.65 (0.33), residues: 262 loop : -0.21 (0.29), residues: 417 =============================================================================== Job complete usr+sys time: 5986.41 seconds wall clock time: 106 minutes 46.54 seconds (6406.54 seconds total)