Starting phenix.real_space_refine on Wed Apr 10 05:35:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/04_2024/7xzz_33535_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/04_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_33535/04_2024/7xzz_33535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/04_2024/7xzz_33535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/04_2024/7xzz_33535_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzz_33535/04_2024/7xzz_33535_neut.pdb" } 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 Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "K TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K ASP 186": "OD1" <-> "OD2" Residue "K GLU 198": "OE1" <-> "OE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 207": "OD1" <-> "OD2" Residue "K ARG 209": "NH1" <-> "NH2" Residue "K GLU 224": "OE1" <-> "OE2" Residue "K GLU 258": "OE1" <-> "OE2" Residue "L TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 186": "OD1" <-> "OD2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L GLU 204": "OE1" <-> "OE2" Residue "L TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 207": "OD1" <-> "OD2" Residue "L ARG 209": "NH1" <-> "NH2" Residue "L GLU 221": "OE1" <-> "OE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 180": "OE1" <-> "OE2" Residue "M ASP 186": "OD1" <-> "OD2" Residue "M GLU 198": "OE1" <-> "OE2" Residue "M GLU 204": "OE1" <-> "OE2" Residue "M TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 207": "OD1" <-> "OD2" Residue "M ARG 209": "NH1" <-> "NH2" Residue "N TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 180": "OE1" <-> "OE2" Residue "N ASP 186": "OD1" <-> "OD2" Residue "N GLU 198": "OE1" <-> "OE2" Residue "N GLU 204": "OE1" <-> "OE2" Residue "N TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 207": "OD1" <-> "OD2" Residue "N ARG 209": "NH1" <-> "NH2" Residue "N GLU 224": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 9.95, per 1000 atoms: 0.53 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 - 3.50 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: 9.12 Conformation dependent library (CDL) restraints added in 2.2 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: 7.63 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: 6.73 Time building geometry restraints manager: 9.68 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: 96.58 - 104.03: 1127 104.03 - 111.48: 9513 111.48 - 118.92: 6636 118.92 - 126.37: 9574 126.37 - 133.82: 990 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 2.520 nonbonded pdb=" NH2 ARG K 202 " pdb=" OE2 GLU K 221 " model vdw 1.930 2.520 nonbonded pdb=" NH2 ARG F 36 " pdb=" OP1 DA J 85 " model vdw 1.962 2.520 nonbonded pdb=" NH2 ARG G 42 " pdb=" O4' DT I 110 " model vdw 1.980 2.520 ... (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 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.440 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 55.930 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.790 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 1.608 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: 0.3354 time to fit residues: 129.0307 Evaluate side-chains 140 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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: 3.9990 chunk 134 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 161 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 263 ASN L 268 ASN L 288 ASN M 288 ASN N 268 ASN N 288 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4682 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.157 19616 Z= 0.383 Angle : 0.720 10.623 27840 Z= 0.409 Chirality : 0.043 0.243 3119 Planarity : 0.005 0.057 2501 Dihedral : 29.029 158.112 5115 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.15 % Allowed : 4.08 % Favored : 95.77 % 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: 1.29 (0.20), residues: 1530 helix: 1.45 (0.19), residues: 620 sheet: 0.52 (0.26), residues: 328 loop : 0.60 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 146 HIS 0.013 0.002 HIS K 193 PHE 0.021 0.002 PHE E 67 TYR 0.016 0.002 TYR H 80 ARG 0.010 0.001 ARG M 175 *********************** 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 168 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.662 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 93 GLN cc_start: 0.9025 (tt0) cc_final: 0.8193 (tp40) REVERT: A 106 ASP cc_start: 0.8368 (m-30) cc_final: 0.7728 (m-30) REVERT: B 68 ASP cc_start: 0.8341 (m-30) cc_final: 0.8130 (m-30) REVERT: C 90 ASP cc_start: 0.8996 (t0) cc_final: 0.8770 (t0) REVERT: E 105 GLU cc_start: 0.8092 (pp20) cc_final: 0.7881 (pp20) REVERT: E 106 ASP cc_start: 0.8114 (m-30) cc_final: 0.7843 (m-30) REVERT: F 97 LEU cc_start: 0.9192 (tp) cc_final: 0.8962 (tt) REVERT: G 38 ASN cc_start: 0.8720 (m-40) cc_final: 0.8026 (t0) REVERT: G 64 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8417 (tm-30) REVERT: G 90 ASP cc_start: 0.8627 (t70) cc_final: 0.8316 (t0) REVERT: K 246 MET cc_start: 0.1130 (mtt) cc_final: -0.0579 (mtm) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.3405 time to fit residues: 83.9306 Evaluate side-chains 114 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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: 5.9990 chunk 134 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 174 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 30.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 168 HIS M 193 HIS M 214 HIS N 168 HIS N 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4747 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 19616 Z= 0.300 Angle : 0.632 7.441 27840 Z= 0.369 Chirality : 0.040 0.184 3119 Planarity : 0.005 0.059 2501 Dihedral : 29.269 158.963 5115 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.22 % Allowed : 3.49 % Favored : 96.29 % 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: 1.48 (0.21), residues: 1530 helix: 1.61 (0.20), residues: 620 sheet: 0.86 (0.28), residues: 304 loop : 0.55 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 146 HIS 0.021 0.002 HIS K 178 PHE 0.021 0.002 PHE G 25 TYR 0.017 0.002 TYR H 37 ARG 0.009 0.001 ARG N 196 *********************** 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 164 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.633 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 93 GLN cc_start: 0.8942 (tt0) cc_final: 0.8682 (tp-100) REVERT: A 106 ASP cc_start: 0.8528 (m-30) cc_final: 0.7852 (m-30) REVERT: B 68 ASP cc_start: 0.8586 (m-30) cc_final: 0.8361 (m-30) REVERT: E 92 LEU cc_start: 0.9357 (tp) cc_final: 0.9081 (tt) REVERT: E 96 CYS cc_start: 0.9076 (m) cc_final: 0.8763 (m) REVERT: K 246 MET cc_start: 0.1695 (mtt) cc_final: -0.0266 (mtm) outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.3552 time to fit residues: 85.1097 Evaluate side-chains 113 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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: 0.3980 chunk 121 optimal weight: 0.3980 chunk 84 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 108 optimal weight: 50.0000 chunk 162 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 154 optimal weight: 40.0000 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 46 HIS L 235 ASN M 239 ASN N 168 HIS N 235 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4747 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 19616 Z= 0.228 Angle : 0.577 8.005 27840 Z= 0.336 Chirality : 0.038 0.171 3119 Planarity : 0.004 0.050 2501 Dihedral : 29.150 162.005 5115 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.62 % 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: 1.59 (0.21), residues: 1530 helix: 1.70 (0.20), residues: 624 sheet: 0.96 (0.29), residues: 304 loop : 0.58 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 146 HIS 0.010 0.001 HIS K 178 PHE 0.029 0.001 PHE E 104 TYR 0.012 0.001 TYR F 88 ARG 0.005 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 158 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8450 (m-30) cc_final: 0.7787 (m-30) REVERT: B 63 GLU cc_start: 0.8987 (tt0) cc_final: 0.8694 (tt0) REVERT: B 68 ASP cc_start: 0.8503 (m-30) cc_final: 0.8302 (m-30) REVERT: E 92 LEU cc_start: 0.9307 (tp) cc_final: 0.8946 (tt) REVERT: E 96 CYS cc_start: 0.9086 (m) cc_final: 0.8612 (m) REVERT: E 103 LEU cc_start: 0.9512 (pp) cc_final: 0.9287 (tt) REVERT: E 106 ASP cc_start: 0.8775 (m-30) cc_final: 0.8072 (m-30) REVERT: G 75 LYS cc_start: 0.8723 (mmpt) cc_final: 0.8516 (mmmt) REVERT: K 160 MET cc_start: 0.5503 (mmm) cc_final: 0.4903 (mtt) REVERT: K 246 MET cc_start: 0.1218 (mtt) cc_final: -0.0457 (mtm) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.3334 time to fit residues: 78.9058 Evaluate side-chains 113 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 40.0000 chunk 146 optimal weight: 6.9990 chunk 118 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 60.0000 chunk 154 optimal weight: 20.0000 chunk 43 optimal weight: 0.1980 chunk 57 optimal weight: 9.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 93 GLN C 31 HIS E 93 GLN G 68 ASN H 46 HIS K 100 GLN K 239 ASN N 214 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4856 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 19616 Z= 0.346 Angle : 0.644 11.241 27840 Z= 0.371 Chirality : 0.040 0.275 3119 Planarity : 0.005 0.050 2501 Dihedral : 29.284 164.411 5115 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: 1.37 (0.21), residues: 1530 helix: 1.42 (0.20), residues: 624 sheet: 0.95 (0.29), residues: 300 loop : 0.52 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 146 HIS 0.009 0.001 HIS A 113 PHE 0.013 0.002 PHE E 67 TYR 0.042 0.002 TYR H 80 ARG 0.014 0.001 ARG M 175 *********************** 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 135 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8420 (m-30) cc_final: 0.7676 (m-30) REVERT: D 97 LEU cc_start: 0.9287 (mt) cc_final: 0.9046 (mt) REVERT: E 94 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8503 (mm-30) REVERT: E 105 GLU cc_start: 0.8328 (pp20) cc_final: 0.8116 (pp20) REVERT: E 106 ASP cc_start: 0.8334 (m-30) cc_final: 0.8057 (m-30) REVERT: E 120 MET cc_start: 0.8699 (mmp) cc_final: 0.8356 (mmm) REVERT: F 63 GLU cc_start: 0.8991 (pm20) cc_final: 0.8772 (mp0) REVERT: F 68 ASP cc_start: 0.9177 (m-30) cc_final: 0.8813 (m-30) REVERT: H 97 LEU cc_start: 0.9417 (mt) cc_final: 0.9188 (mt) REVERT: K 246 MET cc_start: 0.1433 (mtt) cc_final: 0.0087 (mtm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.3339 time to fit residues: 68.0281 Evaluate side-chains 98 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.754 ------------------------------------------------------------------------------- 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: 50.0000 chunk 34 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 172 optimal weight: 40.0000 chunk 142 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 166 optimal weight: 50.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS E 68 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN M 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4802 moved from start: 0.5225 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= 0.211 Angle : 0.574 10.137 27840 Z= 0.333 Chirality : 0.038 0.160 3119 Planarity : 0.004 0.051 2501 Dihedral : 29.339 167.059 5115 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.15 % Allowed : 1.48 % Favored : 98.37 % 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: 1.65 (0.21), residues: 1530 helix: 1.92 (0.20), residues: 619 sheet: 0.91 (0.29), residues: 304 loop : 0.46 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 146 HIS 0.011 0.001 HIS F 75 PHE 0.031 0.002 PHE E 104 TYR 0.029 0.001 TYR H 80 ARG 0.005 0.000 ARG F 78 *********************** 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 142 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8501 (m-30) cc_final: 0.7792 (m-30) REVERT: A 120 MET cc_start: 0.8765 (mmp) cc_final: 0.8179 (mmm) REVERT: B 58 LEU cc_start: 0.9522 (tp) cc_final: 0.9321 (tp) REVERT: C 90 ASP cc_start: 0.8989 (t0) cc_final: 0.8757 (t0) REVERT: D 97 LEU cc_start: 0.9255 (mt) cc_final: 0.8957 (mt) REVERT: E 67 PHE cc_start: 0.9008 (t80) cc_final: 0.8575 (t80) REVERT: E 94 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8695 (mm-30) REVERT: E 105 GLU cc_start: 0.8286 (pp20) cc_final: 0.8025 (pp20) REVERT: E 106 ASP cc_start: 0.8356 (m-30) cc_final: 0.8039 (m-30) REVERT: E 120 MET cc_start: 0.8624 (mmp) cc_final: 0.8159 (mmm) REVERT: G 64 GLU cc_start: 0.9145 (pp20) cc_final: 0.8785 (pp20) REVERT: H 97 LEU cc_start: 0.9351 (mt) cc_final: 0.9149 (mt) REVERT: K 160 MET cc_start: 0.5222 (mmm) cc_final: 0.4921 (mtt) REVERT: N 160 MET cc_start: 0.3771 (tmm) cc_final: 0.2991 (tmm) outliers start: 2 outliers final: 1 residues processed: 141 average time/residue: 0.2989 time to fit residues: 66.2627 Evaluate side-chains 101 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 2.008 ------------------------------------------------------------------------------- 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: 50.0000 chunk 97 optimal weight: 7.9990 chunk 144 optimal weight: 40.0000 chunk 96 optimal weight: 8.9990 chunk 171 optimal weight: 40.0000 chunk 107 optimal weight: 8.9990 chunk 104 optimal weight: 40.0000 chunk 79 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 68 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN L 235 ASN ** M 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4891 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 19616 Z= 0.356 Angle : 0.649 12.618 27840 Z= 0.372 Chirality : 0.040 0.156 3119 Planarity : 0.005 0.051 2501 Dihedral : 29.400 170.906 5115 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % 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: 1.34 (0.21), residues: 1530 helix: 1.49 (0.20), residues: 625 sheet: 0.82 (0.29), residues: 304 loop : 0.43 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 146 HIS 0.028 0.002 HIS M 178 PHE 0.012 0.001 PHE B 61 TYR 0.029 0.002 TYR H 80 ARG 0.007 0.001 ARG M 175 *********************** 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 125 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8849 (tp30) cc_final: 0.8612 (tp30) REVERT: A 106 ASP cc_start: 0.8309 (m-30) cc_final: 0.7569 (m-30) REVERT: A 120 MET cc_start: 0.8767 (mmp) cc_final: 0.8224 (mmm) REVERT: B 63 GLU cc_start: 0.9038 (tt0) cc_final: 0.8293 (tp30) REVERT: D 97 LEU cc_start: 0.9310 (mt) cc_final: 0.9058 (mt) REVERT: E 92 LEU cc_start: 0.9332 (tt) cc_final: 0.9113 (tt) REVERT: E 94 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8895 (mm-30) REVERT: E 96 CYS cc_start: 0.9116 (m) cc_final: 0.8854 (m) REVERT: E 105 GLU cc_start: 0.8336 (pp20) cc_final: 0.8129 (pp20) REVERT: E 106 ASP cc_start: 0.8275 (m-30) cc_final: 0.8032 (m-30) REVERT: E 120 MET cc_start: 0.8728 (mmp) cc_final: 0.8421 (mmm) REVERT: E 123 ASP cc_start: 0.7898 (m-30) cc_final: 0.7500 (m-30) REVERT: F 84 MET cc_start: 0.8761 (tpp) cc_final: 0.8375 (tpp) REVERT: G 75 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8672 (mmmt) REVERT: G 90 ASP cc_start: 0.8686 (t0) cc_final: 0.8275 (t0) REVERT: H 97 LEU cc_start: 0.9399 (mt) cc_final: 0.9141 (mt) REVERT: K 160 MET cc_start: 0.5409 (mmm) cc_final: 0.4985 (mtt) REVERT: N 133 MET cc_start: 0.3083 (ppp) cc_final: 0.2827 (ppp) REVERT: N 160 MET cc_start: 0.4032 (tmm) cc_final: 0.3229 (tmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3106 time to fit residues: 60.6853 Evaluate side-chains 91 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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: 3.9990 chunk 102 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 50.0000 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 134 optimal weight: 50.0000 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN K 235 ASN M 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4873 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 19616 Z= 0.285 Angle : 0.625 12.771 27840 Z= 0.358 Chirality : 0.039 0.165 3119 Planarity : 0.005 0.064 2501 Dihedral : 29.511 175.973 5115 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 1.39 (0.21), residues: 1530 helix: 1.54 (0.20), residues: 624 sheet: 0.83 (0.28), residues: 304 loop : 0.46 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 146 HIS 0.020 0.001 HIS M 178 PHE 0.013 0.001 PHE E 67 TYR 0.027 0.001 TYR H 80 ARG 0.009 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 122 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8794 (tp30) cc_final: 0.8506 (tp30) REVERT: A 106 ASP cc_start: 0.8357 (m-30) cc_final: 0.7738 (m-30) REVERT: A 120 MET cc_start: 0.8812 (mmp) cc_final: 0.8215 (mmm) REVERT: C 90 ASP cc_start: 0.9005 (t0) cc_final: 0.8802 (t0) REVERT: D 97 LEU cc_start: 0.9320 (mt) cc_final: 0.9070 (mt) REVERT: E 90 MET cc_start: 0.8953 (mmm) cc_final: 0.8680 (mmm) REVERT: E 94 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8806 (mm-30) REVERT: E 106 ASP cc_start: 0.8339 (m-30) cc_final: 0.8094 (m-30) REVERT: E 120 MET cc_start: 0.8768 (mmp) cc_final: 0.8423 (mmm) REVERT: E 123 ASP cc_start: 0.7845 (m-30) cc_final: 0.7557 (m-30) REVERT: G 90 ASP cc_start: 0.8645 (t0) cc_final: 0.8270 (t0) REVERT: H 97 LEU cc_start: 0.9376 (mt) cc_final: 0.9135 (mt) REVERT: K 160 MET cc_start: 0.5416 (mmm) cc_final: 0.4915 (mtt) REVERT: N 133 MET cc_start: 0.3325 (ppp) cc_final: 0.3088 (ppp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.3072 time to fit residues: 58.5124 Evaluate side-chains 83 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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: 0.7980 chunk 159 optimal weight: 1.9990 chunk 164 optimal weight: 0.0470 chunk 96 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 112 GLN H 60 ASN N 168 HIS N 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4803 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19616 Z= 0.177 Angle : 0.590 9.675 27840 Z= 0.338 Chirality : 0.038 0.166 3119 Planarity : 0.004 0.057 2501 Dihedral : 29.396 177.176 5115 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % 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: 1.57 (0.21), residues: 1530 helix: 1.76 (0.21), residues: 626 sheet: 0.85 (0.28), residues: 304 loop : 0.52 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 146 HIS 0.015 0.001 HIS M 178 PHE 0.020 0.001 PHE A 104 TYR 0.025 0.001 TYR H 80 ARG 0.003 0.000 ARG E 131 *********************** 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 133 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8823 (tp30) cc_final: 0.8581 (tp30) REVERT: A 106 ASP cc_start: 0.8306 (m-30) cc_final: 0.7755 (m-30) REVERT: A 120 MET cc_start: 0.8830 (mmp) cc_final: 0.8259 (mmm) REVERT: E 103 LEU cc_start: 0.9429 (mm) cc_final: 0.9193 (mm) REVERT: E 106 ASP cc_start: 0.8743 (m-30) cc_final: 0.8055 (m-30) REVERT: E 120 MET cc_start: 0.8710 (mmp) cc_final: 0.8331 (mmm) REVERT: E 123 ASP cc_start: 0.7840 (m-30) cc_final: 0.7604 (m-30) REVERT: G 64 GLU cc_start: 0.9148 (pp20) cc_final: 0.8814 (pp20) REVERT: G 75 LYS cc_start: 0.8820 (mmpt) cc_final: 0.8620 (mmmt) REVERT: G 90 ASP cc_start: 0.8561 (t0) cc_final: 0.8164 (t0) REVERT: H 97 LEU cc_start: 0.9281 (mt) cc_final: 0.8918 (tp) REVERT: K 160 MET cc_start: 0.5428 (mmm) cc_final: 0.4924 (mtt) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.3056 time to fit residues: 62.6652 Evaluate side-chains 89 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 177 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 141 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 86 optimal weight: 50.0000 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 50.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 HIS N 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4955 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.139 19616 Z= 0.448 Angle : 0.714 15.615 27840 Z= 0.404 Chirality : 0.042 0.170 3119 Planarity : 0.005 0.051 2501 Dihedral : 29.513 177.912 5115 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.20 (0.21), residues: 1530 helix: 1.32 (0.20), residues: 626 sheet: 0.75 (0.28), residues: 304 loop : 0.42 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 146 HIS 0.013 0.002 HIS M 178 PHE 0.040 0.002 PHE E 67 TYR 0.036 0.002 TYR B 51 ARG 0.008 0.001 ARG B 45 ********************** 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 112 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8840 (tp30) cc_final: 0.8537 (tp30) REVERT: A 106 ASP cc_start: 0.8347 (m-30) cc_final: 0.7756 (m-30) REVERT: A 120 MET cc_start: 0.8865 (mmp) cc_final: 0.8317 (mmm) REVERT: E 92 LEU cc_start: 0.9159 (tt) cc_final: 0.8943 (tt) REVERT: E 120 MET cc_start: 0.8810 (mmp) cc_final: 0.8528 (mmm) REVERT: E 123 ASP cc_start: 0.7776 (m-30) cc_final: 0.7562 (m-30) REVERT: G 90 ASP cc_start: 0.8561 (t0) cc_final: 0.8187 (t0) REVERT: H 97 LEU cc_start: 0.9436 (mt) cc_final: 0.9006 (tp) REVERT: K 160 MET cc_start: 0.5510 (mmm) cc_final: 0.4967 (mtt) REVERT: M 237 MET cc_start: 0.1007 (ppp) cc_final: 0.0789 (tmm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3340 time to fit residues: 58.8607 Evaluate side-chains 78 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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: 0.9990 chunk 130 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 93 GLN N 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.072572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.035152 restraints weight = 135168.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.035471 restraints weight = 68700.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.035929 restraints weight = 43489.544| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19616 Z= 0.192 Angle : 0.613 11.220 27840 Z= 0.349 Chirality : 0.039 0.177 3119 Planarity : 0.004 0.052 2501 Dihedral : 29.562 176.319 5115 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 1.39 (0.21), residues: 1530 helix: 1.59 (0.20), residues: 628 sheet: 0.77 (0.28), residues: 304 loop : 0.44 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 146 HIS 0.012 0.001 HIS M 178 PHE 0.018 0.001 PHE E 67 TYR 0.025 0.001 TYR H 80 ARG 0.004 0.000 ARG K 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.62 seconds wall clock time: 58 minutes 32.00 seconds (3512.00 seconds total)