Starting phenix.real_space_refine on Tue Nov 19 02:56:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/11_2024/7xzz_33535_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/11_2024/7xzz_33535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/11_2024/7xzz_33535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/11_2024/7xzz_33535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/11_2024/7xzz_33535_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/11_2024/7xzz_33535_neut.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 309 5.49 5 S 78 5.16 5 C 10646 2.51 5 N 3495 2.21 5 O 4095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18623 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 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: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3164 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3183 Classifications: {'DNA': 155} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 154} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "L" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "M" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "N" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Time building chain proxies: 10.78, per 1000 atoms: 0.58 Number of scatterers: 18623 At special positions: 0 Unit cell: (159, 179.14, 120.84, 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 78 16.00 P 309 15.00 O 4095 8.00 N 3495 7.00 C 10646 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 42.9% alpha, 15.2% beta 149 base pairs and 265 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: 4.096A 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 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.293A 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: 4.117A 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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.995A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.538A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.553A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.269A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.524A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 122 Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'K' and resid 277 through 288 Processing helix chain 'K' and resid 289 through 291 No H-bonds generated for 'chain 'K' and resid 289 through 291' Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'L' and resid 277 through 288 Processing helix chain 'L' and resid 289 through 291 No H-bonds generated for 'chain 'L' and resid 289 through 291' Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 277 through 289 Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'N' and resid 277 through 288 Processing helix chain 'N' and resid 289 through 291 No H-bonds generated for 'chain 'N' and resid 289 through 291' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.999A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 removed outlier: 3.757A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.501A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.760A 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: 7.342A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 removed outlier: 3.547A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 6.213A pdb=" N LEU K 257 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG K 267 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE K 255 " --> pdb=" O ARG K 267 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER K 269 " --> pdb=" O THR K 253 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR K 253 " --> pdb=" O SER K 269 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU K 271 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE K 251 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127 removed outlier: 3.803A pdb=" N ILE L 251 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112 Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127 removed outlier: 3.832A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 112 Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127 removed outlier: 3.839A pdb=" N ILE N 251 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 385 hydrogen bonds 762 hydrogen bond angles 0 basepair planarities 149 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3607 1.33 - 1.46: 6509 1.46 - 1.59: 8773 1.59 - 1.71: 615 1.71 - 1.84: 112 Bond restraints: 19616 Sorted by residual: bond pdb=" C PRO L 222 " pdb=" O PRO L 222 " ideal model delta sigma weight residual 1.246 1.213 0.033 8.50e-03 1.38e+04 1.48e+01 bond pdb=" C PRO M 222 " pdb=" O PRO M 222 " ideal model delta sigma weight residual 1.240 1.202 0.039 1.12e-02 7.97e+03 1.19e+01 bond pdb=" CA PRO K 190 " pdb=" C PRO K 190 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.15e+01 bond pdb=" N VAL K 122 " pdb=" CA VAL K 122 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N VAL N 225 " pdb=" CA VAL N 225 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.24e-02 6.50e+03 1.06e+01 ... (remaining 19611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 25847 1.73 - 3.45: 1783 3.45 - 5.18: 182 5.18 - 6.91: 25 6.91 - 8.63: 3 Bond angle restraints: 27840 Sorted by residual: angle pdb=" O PRO L 190 " pdb=" C PRO L 190 " pdb=" N PRO L 191 " ideal model delta sigma weight residual 121.31 123.33 -2.02 4.60e-01 4.73e+00 1.94e+01 angle pdb=" N LEU M 265 " pdb=" CA LEU M 265 " pdb=" C LEU M 265 " ideal model delta sigma weight residual 113.88 108.67 5.21 1.23e+00 6.61e-01 1.79e+01 angle pdb=" O PRO M 190 " pdb=" C PRO M 190 " pdb=" N PRO M 191 " ideal model delta sigma weight residual 121.31 123.17 -1.86 4.60e-01 4.73e+00 1.64e+01 angle pdb=" N GLN E 76 " pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " ideal model delta sigma weight residual 110.32 117.15 -6.83 1.70e+00 3.46e-01 1.61e+01 angle pdb=" O3' DG I 130 " pdb=" C3' DG I 130 " pdb=" C2' DG I 130 " ideal model delta sigma weight residual 111.50 105.57 5.93 1.50e+00 4.44e-01 1.56e+01 ... (remaining 27835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.69: 9129 30.69 - 61.38: 1874 61.38 - 92.07: 67 92.07 - 122.76: 1 122.76 - 153.45: 1 Dihedral angle restraints: 11072 sinusoidal: 6568 harmonic: 4504 Sorted by residual: dihedral pdb=" C4' DC J 33 " pdb=" C3' DC J 33 " pdb=" O3' DC J 33 " pdb=" P DC J 34 " ideal model delta sinusoidal sigma weight residual 220.00 66.55 153.45 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" CA TYR M 236 " pdb=" C TYR M 236 " pdb=" N MET M 237 " pdb=" CA MET M 237 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR K 236 " pdb=" C TYR K 236 " pdb=" N MET K 237 " pdb=" CA MET K 237 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2240 0.052 - 0.103: 618 0.103 - 0.155: 175 0.155 - 0.206: 78 0.206 - 0.258: 8 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CA ARG L 248 " pdb=" N ARG L 248 " pdb=" C ARG L 248 " pdb=" CB ARG L 248 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ARG N 248 " pdb=" N ARG N 248 " pdb=" C ARG N 248 " pdb=" CB ARG N 248 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLU C 61 " pdb=" N GLU C 61 " pdb=" C GLU C 61 " pdb=" CB GLU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 3116 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 52 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C ALA G 52 " 0.077 2.00e-02 2.50e+03 pdb=" O ALA G 52 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA G 53 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.27e+00 pdb=" C LYS F 59 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 19 " 0.030 2.00e-02 2.50e+03 1.26e-02 4.36e+00 pdb=" N9 DA J 19 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA J 19 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DA J 19 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA J 19 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DA J 19 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA J 19 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA J 19 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 19 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA J 19 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA J 19 " -0.004 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 37 2.35 - 2.99: 9024 2.99 - 3.63: 30316 3.63 - 4.26: 49078 4.26 - 4.90: 72886 Nonbonded interactions: 161341 Sorted by model distance: nonbonded pdb=" CD1 LEU G 23 " pdb=" OE1 GLU G 56 " model vdw 1.717 3.460 nonbonded pdb=" NH2 ARG G 17 " pdb=" OP2 DA J 55 " model vdw 1.839 3.120 nonbonded pdb=" NH2 ARG K 202 " pdb=" OE2 GLU K 221 " model vdw 1.930 3.120 nonbonded pdb=" NH2 ARG F 36 " pdb=" OP1 DA J 85 " model vdw 1.962 3.120 nonbonded pdb=" NH2 ARG G 42 " pdb=" O4' DT I 110 " model vdw 1.980 3.120 ... (remaining 161336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 46.600 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4393 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 : 0.006 0.058 19616 Z= 0.357 Angle : 0.915 8.632 27840 Z= 0.608 Chirality : 0.057 0.258 3119 Planarity : 0.005 0.045 2501 Dihedral : 25.147 153.453 8172 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.15 % Allowed : 2.82 % Favored : 97.03 % 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: 0.69 (0.19), residues: 1530 helix: 0.79 (0.18), residues: 629 sheet: 0.45 (0.26), residues: 312 loop : 0.30 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP N 146 HIS 0.010 0.002 HIS K 233 PHE 0.018 0.002 PHE N 270 TYR 0.026 0.003 TYR B 88 ARG 0.007 0.001 ARG M 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8591 (mt) cc_final: 0.8294 (mt) REVERT: A 106 ASP cc_start: 0.8379 (m-30) cc_final: 0.7712 (m-30) REVERT: C 83 LEU cc_start: 0.9529 (mt) cc_final: 0.9047 (mt) REVERT: C 90 ASP cc_start: 0.8989 (t0) cc_final: 0.8760 (t0) REVERT: E 106 ASP cc_start: 0.8567 (m-30) cc_final: 0.7538 (m-30) REVERT: F 68 ASP cc_start: 0.8981 (m-30) cc_final: 0.8700 (p0) REVERT: F 97 LEU cc_start: 0.8977 (tp) cc_final: 0.8683 (tt) REVERT: G 38 ASN cc_start: 0.8115 (m-40) cc_final: 0.7859 (t0) REVERT: G 56 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8229 (mt-10) REVERT: G 64 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8154 (tm-30) outliers start: 2 outliers final: 0 residues processed: 261 average time/residue: 0.3501 time to fit residues: 134.9929 Evaluate side-chains 140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 50.0000 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS K 178 HIS K 268 ASN K 288 ASN L 168 HIS L 268 ASN L 288 ASN M 288 ASN N 168 HIS N 268 ASN N 288 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4710 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.160 19616 Z= 0.407 Angle : 0.737 8.517 27840 Z= 0.419 Chirality : 0.044 0.252 3119 Planarity : 0.006 0.064 2501 Dihedral : 29.087 158.705 5115 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.22 % Allowed : 4.16 % Favored : 95.62 % 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: 1.13 (0.20), residues: 1530 helix: 1.29 (0.19), residues: 620 sheet: 0.54 (0.28), residues: 308 loop : 0.48 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 146 HIS 0.012 0.002 HIS A 113 PHE 0.027 0.002 PHE E 67 TYR 0.018 0.002 TYR A 99 ARG 0.010 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8447 (m-30) cc_final: 0.7763 (m-30) REVERT: B 68 ASP cc_start: 0.8566 (m-30) cc_final: 0.8346 (m-30) REVERT: E 94 GLU cc_start: 0.8685 (tp30) cc_final: 0.8069 (tp30) REVERT: E 105 GLU cc_start: 0.8132 (pp20) cc_final: 0.7877 (pp20) REVERT: E 106 ASP cc_start: 0.8199 (m-30) cc_final: 0.7846 (m-30) REVERT: F 97 LEU cc_start: 0.9262 (tp) cc_final: 0.8973 (tt) REVERT: G 38 ASN cc_start: 0.8683 (m-40) cc_final: 0.8106 (t0) REVERT: G 64 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8414 (tm-30) REVERT: G 90 ASP cc_start: 0.8862 (t70) cc_final: 0.8508 (t0) REVERT: K 246 MET cc_start: 0.0470 (mtt) cc_final: -0.1023 (mtm) outliers start: 3 outliers final: 0 residues processed: 168 average time/residue: 0.3526 time to fit residues: 88.5137 Evaluate side-chains 116 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 0.3980 chunk 174 optimal weight: 50.0000 chunk 144 optimal weight: 6.9990 chunk 160 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN H 46 HIS K 100 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN M 178 HIS M 193 HIS M 239 ASN N 168 HIS N 239 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4671 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19616 Z= 0.221 Angle : 0.589 7.365 27840 Z= 0.344 Chirality : 0.039 0.207 3119 Planarity : 0.004 0.048 2501 Dihedral : 29.169 158.797 5115 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.15 % Allowed : 2.60 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.20), residues: 1530 helix: 1.72 (0.20), residues: 620 sheet: 0.90 (0.28), residues: 304 loop : 0.53 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 146 HIS 0.021 0.001 HIS K 178 PHE 0.019 0.001 PHE G 25 TYR 0.016 0.001 TYR F 88 ARG 0.004 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9125 (tt0) cc_final: 0.8709 (tp40) REVERT: A 94 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8132 (mm-30) REVERT: A 106 ASP cc_start: 0.8567 (m-30) cc_final: 0.7824 (m-30) REVERT: B 68 ASP cc_start: 0.8463 (m-30) cc_final: 0.8213 (m-30) REVERT: E 92 LEU cc_start: 0.9268 (tp) cc_final: 0.8968 (tt) REVERT: E 96 CYS cc_start: 0.9023 (m) cc_final: 0.8718 (m) REVERT: E 105 GLU cc_start: 0.8114 (pp20) cc_final: 0.7879 (pp20) REVERT: E 106 ASP cc_start: 0.8243 (m-30) cc_final: 0.7885 (m-30) REVERT: F 97 LEU cc_start: 0.9156 (tp) cc_final: 0.8955 (tt) REVERT: G 38 ASN cc_start: 0.8854 (m-40) cc_final: 0.8162 (t0) REVERT: G 75 LYS cc_start: 0.8655 (mmpt) cc_final: 0.8382 (mmmm) REVERT: G 90 ASP cc_start: 0.8849 (t70) cc_final: 0.8513 (t70) REVERT: K 246 MET cc_start: 0.1467 (mtt) cc_final: 0.0639 (mtt) REVERT: N 160 MET cc_start: 0.3368 (tmm) cc_final: 0.2967 (tmm) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.3334 time to fit residues: 85.0849 Evaluate side-chains 120 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 0.0980 chunk 121 optimal weight: 0.0020 chunk 84 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 108 optimal weight: 40.0000 chunk 162 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN L 239 ASN M 178 HIS N 168 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4667 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19616 Z= 0.191 Angle : 0.574 6.086 27840 Z= 0.334 Chirality : 0.038 0.179 3119 Planarity : 0.004 0.050 2501 Dihedral : 29.033 160.737 5115 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.15 % Allowed : 2.30 % Favored : 97.55 % 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: 1.61 (0.21), residues: 1530 helix: 1.76 (0.20), residues: 625 sheet: 0.97 (0.29), residues: 304 loop : 0.52 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 146 HIS 0.022 0.001 HIS M 178 PHE 0.014 0.001 PHE G 25 TYR 0.030 0.001 TYR H 80 ARG 0.006 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8521 (m-30) cc_final: 0.8016 (t70) REVERT: B 68 ASP cc_start: 0.8430 (m-30) cc_final: 0.8190 (m-30) REVERT: E 92 LEU cc_start: 0.9243 (tp) cc_final: 0.8939 (tt) REVERT: E 96 CYS cc_start: 0.8992 (m) cc_final: 0.8419 (m) REVERT: E 103 LEU cc_start: 0.9459 (pp) cc_final: 0.9240 (tt) REVERT: E 105 GLU cc_start: 0.8138 (pp20) cc_final: 0.7909 (pp20) REVERT: E 106 ASP cc_start: 0.8265 (m-30) cc_final: 0.7873 (m-30) REVERT: F 97 LEU cc_start: 0.9135 (tp) cc_final: 0.8921 (tt) REVERT: G 38 ASN cc_start: 0.8790 (m-40) cc_final: 0.8468 (p0) REVERT: G 75 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8428 (mmmm) REVERT: K 246 MET cc_start: 0.1395 (mtt) cc_final: -0.0026 (mtm) REVERT: N 160 MET cc_start: 0.3580 (tmm) cc_final: 0.3151 (tmm) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.3247 time to fit residues: 83.6810 Evaluate side-chains 119 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 50.0000 chunk 70 optimal weight: 0.8980 chunk 146 optimal weight: 30.0000 chunk 118 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 50.0000 chunk 154 optimal weight: 50.0000 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 3.0984 ------------------------------------------------------------------------------- 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** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4740 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 19616 Z= 0.260 Angle : 0.593 8.190 27840 Z= 0.343 Chirality : 0.038 0.181 3119 Planarity : 0.004 0.051 2501 Dihedral : 28.992 162.729 5115 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 1.58 (0.21), residues: 1530 helix: 1.69 (0.20), residues: 625 sheet: 0.99 (0.29), residues: 304 loop : 0.54 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 146 HIS 0.012 0.001 HIS K 178 PHE 0.032 0.002 PHE A 67 TYR 0.031 0.001 TYR H 80 ARG 0.010 0.000 ARG L 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8529 (m-30) cc_final: 0.7754 (m-30) REVERT: B 84 MET cc_start: 0.8580 (tpt) cc_final: 0.8300 (tpp) REVERT: E 92 LEU cc_start: 0.9209 (tp) cc_final: 0.8947 (tt) REVERT: E 96 CYS cc_start: 0.8996 (m) cc_final: 0.8482 (m) REVERT: E 105 GLU cc_start: 0.8262 (pp20) cc_final: 0.8060 (pp20) REVERT: E 106 ASP cc_start: 0.8260 (m-30) cc_final: 0.7927 (m-30) REVERT: E 120 MET cc_start: 0.8567 (mmp) cc_final: 0.8260 (mmm) REVERT: F 63 GLU cc_start: 0.8922 (pm20) cc_final: 0.8701 (mp0) REVERT: F 84 MET cc_start: 0.8592 (tpp) cc_final: 0.8350 (tpp) REVERT: F 97 LEU cc_start: 0.9226 (tp) cc_final: 0.9010 (tt) REVERT: G 68 ASN cc_start: 0.8691 (m-40) cc_final: 0.8422 (m110) REVERT: G 75 LYS cc_start: 0.8739 (mmpt) cc_final: 0.8487 (mmmm) REVERT: G 90 ASP cc_start: 0.8825 (t70) cc_final: 0.8430 (t70) REVERT: K 246 MET cc_start: 0.1581 (mtt) cc_final: 0.0069 (mtm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3339 time to fit residues: 78.6539 Evaluate side-chains 117 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4766 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 19616 Z= 0.245 Angle : 0.585 9.604 27840 Z= 0.339 Chirality : 0.038 0.161 3119 Planarity : 0.004 0.052 2501 Dihedral : 29.050 164.425 5115 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.92 % 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: 1.63 (0.21), residues: 1530 helix: 1.79 (0.20), residues: 626 sheet: 0.95 (0.29), residues: 304 loop : 0.54 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 146 HIS 0.012 0.001 HIS K 178 PHE 0.012 0.001 PHE N 109 TYR 0.022 0.001 TYR H 80 ARG 0.028 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8422 (mm-30) REVERT: A 97 GLU cc_start: 0.8708 (pp20) cc_final: 0.8424 (pp20) REVERT: A 106 ASP cc_start: 0.8512 (m-30) cc_final: 0.7676 (m-30) REVERT: A 120 MET cc_start: 0.8781 (mmp) cc_final: 0.8309 (mmm) REVERT: B 68 ASP cc_start: 0.8624 (m-30) cc_final: 0.8396 (m-30) REVERT: B 84 MET cc_start: 0.8676 (tpt) cc_final: 0.8352 (tpp) REVERT: E 92 LEU cc_start: 0.9237 (tp) cc_final: 0.8938 (tt) REVERT: E 96 CYS cc_start: 0.9046 (m) cc_final: 0.8536 (m) REVERT: E 105 GLU cc_start: 0.8230 (pp20) cc_final: 0.8028 (pp20) REVERT: E 106 ASP cc_start: 0.8259 (m-30) cc_final: 0.7962 (m-30) REVERT: E 120 MET cc_start: 0.8587 (mmp) cc_final: 0.8202 (mmm) REVERT: F 84 MET cc_start: 0.8579 (tpp) cc_final: 0.8314 (tpp) REVERT: F 97 LEU cc_start: 0.9230 (tp) cc_final: 0.9029 (tt) REVERT: G 64 GLU cc_start: 0.9053 (pp20) cc_final: 0.8800 (pp20) REVERT: G 75 LYS cc_start: 0.8740 (mmpt) cc_final: 0.8520 (mmmm) REVERT: K 246 MET cc_start: 0.1582 (mtt) cc_final: -0.0138 (mtm) REVERT: N 133 MET cc_start: 0.3154 (ppp) cc_final: 0.2945 (ppp) outliers start: 1 outliers final: 1 residues processed: 155 average time/residue: 0.3157 time to fit residues: 75.3210 Evaluate side-chains 116 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 144 optimal weight: 0.0870 chunk 96 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 HIS N 168 HIS N 214 HIS N 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4846 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 19616 Z= 0.297 Angle : 0.637 13.347 27840 Z= 0.363 Chirality : 0.040 0.185 3119 Planarity : 0.005 0.051 2501 Dihedral : 29.226 168.950 5115 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 1.43 (0.21), residues: 1530 helix: 1.61 (0.20), residues: 621 sheet: 0.85 (0.29), residues: 304 loop : 0.46 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 146 HIS 0.012 0.001 HIS K 178 PHE 0.014 0.002 PHE A 104 TYR 0.029 0.002 TYR H 80 ARG 0.009 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8422 (mm-30) REVERT: A 97 GLU cc_start: 0.8776 (pp20) cc_final: 0.8491 (pp20) REVERT: A 106 ASP cc_start: 0.8400 (m-30) cc_final: 0.7811 (m-30) REVERT: A 120 MET cc_start: 0.8766 (mmp) cc_final: 0.8209 (mmm) REVERT: B 68 ASP cc_start: 0.8690 (m-30) cc_final: 0.8380 (m-30) REVERT: B 84 MET cc_start: 0.8797 (tpt) cc_final: 0.8440 (tpp) REVERT: D 97 LEU cc_start: 0.9247 (mt) cc_final: 0.8898 (mt) REVERT: E 106 ASP cc_start: 0.8182 (m-30) cc_final: 0.7964 (m-30) REVERT: E 120 MET cc_start: 0.8622 (mmp) cc_final: 0.8132 (mmm) REVERT: G 68 ASN cc_start: 0.9258 (m-40) cc_final: 0.8839 (m110) REVERT: K 246 MET cc_start: 0.1876 (mtt) cc_final: 0.0216 (mtm) REVERT: N 160 MET cc_start: 0.4053 (tmm) cc_final: 0.3501 (tmm) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.3206 time to fit residues: 69.8642 Evaluate side-chains 102 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.0070 chunk 102 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 109 optimal weight: 0.0470 chunk 116 optimal weight: 30.0000 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 233 HIS N 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4747 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19616 Z= 0.168 Angle : 0.593 12.873 27840 Z= 0.338 Chirality : 0.038 0.167 3119 Planarity : 0.004 0.064 2501 Dihedral : 29.166 171.070 5115 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 1.55 (0.21), residues: 1530 helix: 1.70 (0.20), residues: 624 sheet: 0.90 (0.29), residues: 300 loop : 0.54 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 146 HIS 0.010 0.001 HIS K 178 PHE 0.030 0.001 PHE E 104 TYR 0.017 0.001 TYR G 39 ARG 0.007 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8300 (mm-30) REVERT: A 97 GLU cc_start: 0.8677 (pp20) cc_final: 0.8369 (pp20) REVERT: A 106 ASP cc_start: 0.8383 (m-30) cc_final: 0.7983 (m-30) REVERT: A 120 MET cc_start: 0.8758 (mmp) cc_final: 0.8168 (mmm) REVERT: B 68 ASP cc_start: 0.8607 (m-30) cc_final: 0.8319 (m-30) REVERT: B 84 MET cc_start: 0.8721 (tpt) cc_final: 0.8324 (mmm) REVERT: D 97 LEU cc_start: 0.9194 (mt) cc_final: 0.8934 (mt) REVERT: E 96 CYS cc_start: 0.9046 (m) cc_final: 0.8744 (m) REVERT: E 103 LEU cc_start: 0.9511 (mm) cc_final: 0.9310 (mm) REVERT: E 106 ASP cc_start: 0.8680 (m-30) cc_final: 0.7438 (m-30) REVERT: E 120 MET cc_start: 0.8592 (mmp) cc_final: 0.8074 (mmm) REVERT: G 64 GLU cc_start: 0.9151 (pp20) cc_final: 0.8817 (pp20) REVERT: G 68 ASN cc_start: 0.9236 (m-40) cc_final: 0.8542 (m110) REVERT: K 246 MET cc_start: 0.1756 (mtt) cc_final: 0.0366 (mtm) REVERT: N 133 MET cc_start: 0.3101 (ppp) cc_final: 0.2887 (ppp) REVERT: N 160 MET cc_start: 0.3777 (tmm) cc_final: 0.3061 (tmm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3137 time to fit residues: 73.8183 Evaluate side-chains 107 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 164 optimal weight: 50.0000 chunk 96 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 151 optimal weight: 40.0000 chunk 104 optimal weight: 5.9990 chunk 169 optimal weight: 50.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4841 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 19616 Z= 0.296 Angle : 0.626 11.869 27840 Z= 0.358 Chirality : 0.039 0.152 3119 Planarity : 0.004 0.051 2501 Dihedral : 29.133 173.605 5115 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 1.51 (0.21), residues: 1530 helix: 1.66 (0.20), residues: 630 sheet: 0.85 (0.29), residues: 300 loop : 0.52 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 146 HIS 0.012 0.001 HIS K 178 PHE 0.016 0.001 PHE E 104 TYR 0.046 0.001 TYR H 80 ARG 0.004 0.000 ARG L 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 97 GLU cc_start: 0.8783 (pp20) cc_final: 0.8490 (pp20) REVERT: A 120 MET cc_start: 0.8829 (mmp) cc_final: 0.8253 (mmm) REVERT: B 68 ASP cc_start: 0.8748 (m-30) cc_final: 0.8470 (m-30) REVERT: B 84 MET cc_start: 0.8837 (tpt) cc_final: 0.8554 (tpp) REVERT: D 97 LEU cc_start: 0.9297 (mt) cc_final: 0.9065 (mt) REVERT: E 92 LEU cc_start: 0.9288 (tt) cc_final: 0.9002 (tt) REVERT: E 94 GLU cc_start: 0.9140 (tt0) cc_final: 0.8710 (tt0) REVERT: E 96 CYS cc_start: 0.9106 (m) cc_final: 0.8790 (m) REVERT: E 103 LEU cc_start: 0.9510 (mm) cc_final: 0.9214 (mm) REVERT: E 120 MET cc_start: 0.8675 (mmp) cc_final: 0.8126 (mmm) REVERT: G 64 GLU cc_start: 0.9183 (pp20) cc_final: 0.8690 (pp20) REVERT: G 68 ASN cc_start: 0.9245 (m-40) cc_final: 0.8548 (m110) REVERT: G 75 LYS cc_start: 0.8687 (mmpt) cc_final: 0.8443 (mmmm) REVERT: K 246 MET cc_start: 0.1920 (mtt) cc_final: 0.0746 (mtt) REVERT: N 133 MET cc_start: 0.3307 (ppp) cc_final: 0.3088 (ppp) REVERT: N 160 MET cc_start: 0.3889 (tmm) cc_final: 0.3444 (tmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2997 time to fit residues: 61.5653 Evaluate side-chains 99 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 50.0000 chunk 80 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 86 optimal weight: 50.0000 chunk 112 optimal weight: 0.0070 chunk 150 optimal weight: 9.9990 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS K 214 HIS L 235 ASN M 100 GLN N 233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4906 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 19616 Z= 0.354 Angle : 0.675 14.570 27840 Z= 0.383 Chirality : 0.041 0.192 3119 Planarity : 0.005 0.050 2501 Dihedral : 29.438 179.542 5115 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.27 (0.21), residues: 1530 helix: 1.42 (0.20), residues: 625 sheet: 0.74 (0.29), residues: 300 loop : 0.44 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 146 HIS 0.011 0.001 HIS K 178 PHE 0.023 0.002 PHE E 104 TYR 0.052 0.002 TYR H 80 ARG 0.013 0.001 ARG N 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8391 (mm-30) REVERT: A 97 GLU cc_start: 0.8822 (pp20) cc_final: 0.8545 (pp20) REVERT: A 106 ASP cc_start: 0.8398 (m-30) cc_final: 0.7788 (m-30) REVERT: A 120 MET cc_start: 0.8760 (mmp) cc_final: 0.8280 (mmm) REVERT: B 68 ASP cc_start: 0.8866 (m-30) cc_final: 0.8644 (m-30) REVERT: B 84 MET cc_start: 0.8867 (tpt) cc_final: 0.8563 (tpp) REVERT: D 97 LEU cc_start: 0.9295 (mt) cc_final: 0.9038 (mt) REVERT: E 92 LEU cc_start: 0.9295 (tt) cc_final: 0.9031 (tt) REVERT: E 96 CYS cc_start: 0.9117 (m) cc_final: 0.8810 (m) REVERT: E 103 LEU cc_start: 0.9453 (mm) cc_final: 0.9169 (mm) REVERT: E 106 ASP cc_start: 0.8668 (m-30) cc_final: 0.7573 (m-30) REVERT: E 120 MET cc_start: 0.8702 (mmp) cc_final: 0.8119 (mmm) REVERT: K 246 MET cc_start: 0.2149 (mtt) cc_final: 0.0954 (mtt) REVERT: L 160 MET cc_start: 0.2546 (ppp) cc_final: 0.2344 (ppp) REVERT: N 160 MET cc_start: 0.3945 (tmm) cc_final: 0.3504 (tmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3149 time to fit residues: 59.0973 Evaluate side-chains 86 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 124 optimal weight: 40.0000 chunk 8 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN F 27 GLN N 168 HIS N 233 HIS N 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.072881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.035747 restraints weight = 132148.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.035801 restraints weight = 66565.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.035968 restraints weight = 42563.995| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19616 Z= 0.177 Angle : 0.603 11.004 27840 Z= 0.342 Chirality : 0.039 0.173 3119 Planarity : 0.004 0.052 2501 Dihedral : 29.326 178.596 5115 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 1.46 (0.21), residues: 1530 helix: 1.64 (0.20), residues: 625 sheet: 0.84 (0.29), residues: 300 loop : 0.47 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 146 HIS 0.011 0.001 HIS K 178 PHE 0.012 0.001 PHE G 25 TYR 0.034 0.001 TYR H 80 ARG 0.014 0.000 ARG M 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3293.26 seconds wall clock time: 62 minutes 7.27 seconds (3727.27 seconds total)