Starting phenix.real_space_refine (version: dev) on Sat May 14 15:42:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/05_2022/7k61_22686.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/05_2022/7k61_22686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/05_2022/7k61_22686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/05_2022/7k61_22686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/05_2022/7k61_22686.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/05_2022/7k61_22686.pdb" } resolution = 2.85 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= 0.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 17723 Number of models: 1 Model: "" Number of chains: 12 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 Time building chain proxies: 9.72, per 1000 atoms: 0.55 Number of scatterers: 17723 At special positions: 0 Unit cell: (131.886, 122.314, 195.702, 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 4150 8.00 N 3243 7.00 C 9904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.03 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 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: 8.07 Conformation dependent library (CDL) restraints added in 1.7 seconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 22 sheets defined 48.4% alpha, 21.7% beta 197 base pairs and 347 stacking pairs defined. Time for finding SS restraints: 7.85 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.891A 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 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.593A 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: 3.533A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (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: 4.221A 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 removed outlier: 3.709A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.599A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.559A 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 74 removed outlier: 4.251A 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 103 through 124 removed outlier: 3.634A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.607A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) 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: 3.649A 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: 3.580A 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 sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.593A 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 96 through 98 removed outlier: 6.415A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.051A 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 100 through 102 removed outlier: 6.502A 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: 6.739A 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: 7.021A 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: 3.702A 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: 6.365A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.413A 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: 6.365A 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: 6.089A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.714A 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: 6.089A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 3.925A 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 24 removed outlier: 3.555A 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: 6.628A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.435A 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: 6.483A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.728A 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: 3.800A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 347 stacking parallelities Total time for adding SS restraints: 7.44 Time building geometry restraints manager: 8.63 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: 3737 1.33 - 1.45: 6089 1.45 - 1.57: 8206 1.57 - 1.69: 786 1.69 - 1.82: 52 Bond restraints: 18870 Sorted by residual: bond pdb=" CA ASN G 89 " pdb=" C ASN G 89 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.80e-02 3.09e+03 3.03e+00 bond pdb=" CB THR H 52 " pdb=" CG2 THR H 52 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG1 ILE C 62 " pdb=" CD1 ILE C 62 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.36e+00 bond pdb=" CG1 ILE D 61 " pdb=" CD1 ILE D 61 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 bond pdb=" CB PRO E 66 " pdb=" CG PRO E 66 " ideal model delta sigma weight residual 1.492 1.424 0.068 5.00e-02 4.00e+02 1.86e+00 ... (remaining 18865 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.66: 1567 104.66 - 112.00: 10497 112.00 - 119.33: 5567 119.33 - 126.66: 8380 126.66 - 134.00: 1186 Bond angle restraints: 27197 Sorted by residual: angle pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " pdb=" CG ASN G 73 " ideal model delta sigma weight residual 112.60 115.50 -2.90 1.00e+00 1.00e+00 8.42e+00 angle pdb=" N GLN N 88 " pdb=" CA GLN N 88 " pdb=" C GLN N 88 " ideal model delta sigma weight residual 114.31 110.82 3.49 1.29e+00 6.01e-01 7.34e+00 angle pdb=" C TYR N 69 " pdb=" N ALA N 70 " pdb=" CA ALA N 70 " ideal model delta sigma weight residual 121.54 126.44 -4.90 1.91e+00 2.74e-01 6.59e+00 angle pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta sigma weight residual 122.15 114.90 7.25 2.83e+00 1.25e-01 6.56e+00 angle pdb=" N ASN G 73 " pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 113.28 110.18 3.10 1.22e+00 6.72e-01 6.48e+00 ... (remaining 27192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 8037 35.34 - 70.68: 1891 70.68 - 106.02: 20 106.02 - 141.35: 0 141.35 - 176.69: 2 Dihedral angle restraints: 9950 sinusoidal: 6404 harmonic: 3546 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+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 43.31 176.69 1 3.50e+01 8.16e-04 1.57e+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 69.48 150.52 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 9947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1923 0.035 - 0.069: 879 0.069 - 0.104: 198 0.104 - 0.138: 58 0.138 - 0.173: 6 Chirality restraints: 3064 Sorted by residual: 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 7.47e-01 chirality pdb=" CA SER M 113 " pdb=" N SER M 113 " pdb=" C SER M 113 " pdb=" CB SER M 113 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CB THR M 102 " pdb=" CA THR M 102 " pdb=" OG1 THR M 102 " pdb=" CG2 THR M 102 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 3061 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 201 " -0.021 2.00e-02 2.50e+03 2.01e-02 8.06e+00 pdb=" CG TYR N 201 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR N 201 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR N 201 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR N 201 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR N 201 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR N 201 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR N 201 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 73 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C ASN G 73 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN G 73 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 74 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO D 103 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.027 5.00e-02 4.00e+02 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 630 2.68 - 3.24: 15654 3.24 - 3.79: 34537 3.79 - 4.35: 44656 4.35 - 4.90: 63674 Nonbonded interactions: 159151 Sorted by model distance: nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.130 2.440 nonbonded pdb=" NH1 ARG H 31 " pdb=" OP1 DG J 150 " model vdw 2.207 2.520 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR H 52 " model vdw 2.217 2.440 nonbonded pdb=" NH2 ARG G 32 " pdb=" OE1 GLU H 35 " model vdw 2.271 2.520 nonbonded pdb=" O THR C 76 " pdb=" OG1 THR D 52 " model vdw 2.280 2.440 ... (remaining 159146 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 9904 2.51 5 N 3243 2.21 5 O 4150 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 8.610 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.150 Process input model: 55.090 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.007 0.068 18870 Z= 0.433 Angle : 0.669 7.247 27197 Z= 0.401 Chirality : 0.041 0.173 3064 Planarity : 0.004 0.049 2066 Dihedral : 27.287 176.693 7666 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 1.15 (0.24), residues: 1198 helix: 1.55 (0.21), residues: 550 sheet: 0.29 (0.34), residues: 242 loop : 0.13 (0.30), residues: 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.284 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 240 average time/residue: 1.6995 time to fit residues: 442.2989 Evaluate side-chains 193 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2681 time to fit residues: 2.4390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 120 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 113 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 18870 Z= 0.226 Angle : 0.564 6.941 27197 Z= 0.334 Chirality : 0.035 0.142 3064 Planarity : 0.004 0.050 2066 Dihedral : 30.781 176.144 5310 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.93 % 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: 1198 helix: 2.15 (0.21), residues: 552 sheet: 0.46 (0.33), residues: 240 loop : 0.29 (0.31), residues: 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 1.439 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 219 average time/residue: 1.7724 time to fit residues: 422.2981 Evaluate side-chains 206 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 7 average time/residue: 0.7984 time to fit residues: 8.2115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 75 HIS D 47 GLN D 84 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN M 110 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 18870 Z= 0.424 Angle : 0.611 7.376 27197 Z= 0.355 Chirality : 0.039 0.155 3064 Planarity : 0.004 0.045 2066 Dihedral : 31.044 178.337 5310 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 3.18 % 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: 1.59 (0.24), residues: 1198 helix: 1.99 (0.21), residues: 552 sheet: 0.45 (0.33), residues: 240 loop : 0.25 (0.31), residues: 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 1.513 Fit side-chains outliers start: 33 outliers final: 15 residues processed: 218 average time/residue: 1.6308 time to fit residues: 387.4109 Evaluate side-chains 220 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 5 residues processed: 11 average time/residue: 0.7727 time to fit residues: 11.6579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 30.0000 chunk 15 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN N 152 GLN N 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 18870 Z= 0.265 Angle : 0.559 6.847 27197 Z= 0.329 Chirality : 0.035 0.137 3064 Planarity : 0.004 0.043 2066 Dihedral : 30.894 178.077 5310 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 2.31 % 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: 1198 helix: 2.23 (0.21), residues: 552 sheet: 0.56 (0.33), residues: 240 loop : 0.36 (0.32), residues: 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 1.570 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 215 average time/residue: 1.6509 time to fit residues: 386.9339 Evaluate side-chains 207 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 10 average time/residue: 0.7110 time to fit residues: 10.2292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 127 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 18870 Z= 0.179 Angle : 0.531 6.712 27197 Z= 0.315 Chirality : 0.033 0.130 3064 Planarity : 0.003 0.044 2066 Dihedral : 30.496 178.766 5310 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 2.31 % 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: 2.16 (0.24), residues: 1198 helix: 2.56 (0.21), residues: 552 sheet: 0.78 (0.34), residues: 230 loop : 0.34 (0.31), residues: 416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 1.562 Fit side-chains outliers start: 24 outliers final: 6 residues processed: 210 average time/residue: 1.5589 time to fit residues: 358.7464 Evaluate side-chains 196 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.7153 time to fit residues: 3.3854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 0.0020 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 104 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 18870 Z= 0.200 Angle : 0.535 9.644 27197 Z= 0.316 Chirality : 0.033 0.132 3064 Planarity : 0.003 0.042 2066 Dihedral : 30.551 179.160 5310 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.24), residues: 1198 helix: 2.61 (0.21), residues: 552 sheet: 0.72 (0.34), residues: 240 loop : 0.45 (0.31), residues: 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 1.499 Fit side-chains outliers start: 26 outliers final: 10 residues processed: 207 average time/residue: 1.6223 time to fit residues: 366.7049 Evaluate side-chains 207 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 1.422 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 5 average time/residue: 0.5551 time to fit residues: 5.1690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 92 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 91 optimal weight: 30.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN M 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 18870 Z= 0.424 Angle : 0.603 8.528 27197 Z= 0.348 Chirality : 0.039 0.150 3064 Planarity : 0.004 0.038 2066 Dihedral : 30.991 178.380 5310 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.24), residues: 1198 helix: 2.19 (0.22), residues: 552 sheet: 0.61 (0.33), residues: 240 loop : 0.35 (0.31), residues: 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 1.549 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 203 average time/residue: 1.6524 time to fit residues: 365.7285 Evaluate side-chains 205 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 6 average time/residue: 0.4618 time to fit residues: 5.3185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN F 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 18870 Z= 0.218 Angle : 0.567 9.183 27197 Z= 0.333 Chirality : 0.035 0.143 3064 Planarity : 0.004 0.035 2066 Dihedral : 31.032 178.833 5310 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.64 % 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: 1.89 (0.24), residues: 1198 helix: 2.25 (0.22), residues: 552 sheet: 0.76 (0.34), residues: 230 loop : 0.28 (0.31), residues: 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 1.441 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 215 average time/residue: 1.5992 time to fit residues: 376.0847 Evaluate side-chains 206 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 197 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.8333 time to fit residues: 5.4210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 18870 Z= 0.241 Angle : 0.555 6.268 27197 Z= 0.327 Chirality : 0.035 0.134 3064 Planarity : 0.004 0.058 2066 Dihedral : 30.859 178.941 5310 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 1.35 % 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: 1.98 (0.24), residues: 1198 helix: 2.34 (0.22), residues: 552 sheet: 0.64 (0.33), residues: 240 loop : 0.41 (0.31), residues: 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 1.516 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 201 average time/residue: 1.6282 time to fit residues: 357.5195 Evaluate side-chains 197 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.1956 time to fit residues: 2.9934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 18870 Z= 0.272 Angle : 0.561 11.200 27197 Z= 0.328 Chirality : 0.035 0.134 3064 Planarity : 0.004 0.037 2066 Dihedral : 30.767 178.387 5310 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.06 % 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: 1.96 (0.24), residues: 1198 helix: 2.34 (0.22), residues: 550 sheet: 0.81 (0.34), residues: 230 loop : 0.25 (0.31), residues: 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 1.495 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 198 average time/residue: 1.6373 time to fit residues: 353.6983 Evaluate side-chains 198 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 191 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2725 time to fit residues: 2.0616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** A 125 GLN F 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.126832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078716 restraints weight = 30870.105| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.47 r_work: 0.3035 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work: 0.3011 rms_B_bonded: 1.40 restraints_weight: 0.1250 r_work: 0.2998 rms_B_bonded: 1.50 restraints_weight: 0.0625 r_work: 0.2985 rms_B_bonded: 1.63 restraints_weight: 0.0312 r_work: 0.2971 rms_B_bonded: 1.78 restraints_weight: 0.0156 r_work: 0.2957 rms_B_bonded: 1.96 restraints_weight: 0.0078 r_work: 0.2941 rms_B_bonded: 2.17 restraints_weight: 0.0039 r_work: 0.2924 rms_B_bonded: 2.41 restraints_weight: 0.0020 r_work: 0.2906 rms_B_bonded: 2.67 restraints_weight: 0.0010 r_work: 0.2887 rms_B_bonded: 2.97 restraints_weight: 0.0005 r_work: 0.2866 rms_B_bonded: 3.29 restraints_weight: 0.0002 r_work: 0.2844 rms_B_bonded: 3.66 restraints_weight: 0.0001 r_work: 0.2819 rms_B_bonded: 4.07 restraints_weight: 0.0001 r_work: 0.2793 rms_B_bonded: 4.52 restraints_weight: 0.0000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 18870 Z= 0.206 Angle : 0.553 11.839 27197 Z= 0.325 Chirality : 0.034 0.140 3064 Planarity : 0.004 0.049 2066 Dihedral : 30.775 178.373 5310 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.16 % 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: 2.03 (0.24), residues: 1198 helix: 2.42 (0.22), residues: 550 sheet: 0.82 (0.34), residues: 230 loop : 0.27 (0.31), residues: 418 =============================================================================== Job complete usr+sys time: 5873.49 seconds wall clock time: 104 minutes 54.58 seconds (6294.58 seconds total)