Starting phenix.real_space_refine on Mon Mar 18 09:32:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k63_22687/03_2024/7k63_22687.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k63_22687/03_2024/7k63_22687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k63_22687/03_2024/7k63_22687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k63_22687/03_2024/7k63_22687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k63_22687/03_2024/7k63_22687.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k63_22687/03_2024/7k63_22687.pdb" } resolution = 3.03 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic. 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 394 5.49 5 S 32 5.16 5 C 10288 2.51 5 N 3355 2.21 5 O 4261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 20": "OD1" <-> "OD2" Residue "M ARG 37": "NH1" <-> "NH2" Residue "M ASP 75": "OD1" <-> "OD2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "M ASP 101": "OD1" <-> "OD2" Residue "M TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M GLU 238": "OE1" <-> "OE2" Residue "M ASP 257": "OD1" <-> "OD2" Residue "M TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 36": "OE1" <-> "OE2" Residue "N ARG 37": "NH1" <-> "NH2" Residue "N TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "N PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 101": "OD1" <-> "OD2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "N GLU 195": "OE1" <-> "OE2" Residue "N TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 222": "OD1" <-> "OD2" Residue "N TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 238": "OE1" <-> "OE2" Residue "U TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 53": "OE1" <-> "OE2" Residue "U TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 99": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18330 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4015 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "J" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4062 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "U" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 607 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Time building chain proxies: 9.09, per 1000 atoms: 0.50 Number of scatterers: 18330 At special positions: 0 Unit cell: (131.62, 123.643, 196.766, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 394 15.00 O 4261 8.00 N 3355 7.00 C 10288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.57 Conformation dependent library (CDL) restraints added in 1.8 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 23 sheets defined 48.8% alpha, 20.6% beta 197 base pairs and 334 stacking pairs defined. Time for finding SS restraints: 8.34 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.559A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.950A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.156A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (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 removed outlier: 3.602A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.567A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.255A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.540A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.899A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.709A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 removed outlier: 3.514A pdb=" N THR N 102 " --> pdb=" O SER N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.717A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing helix chain 'U' and resid 45 through 59 removed outlier: 3.800A pdb=" N ARG U 56 " --> pdb=" O VAL U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 74 Processing helix chain 'U' and resid 83 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.067A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.486A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.632A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.996A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.699A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER M 91 " --> pdb=" O SER M 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.849A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 32 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.849A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 32 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.555A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 3.996A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.757A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.615A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.944A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 64 through 65 617 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 334 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 9.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3676 1.33 - 1.45: 6202 1.45 - 1.57: 8770 1.57 - 1.69: 786 1.69 - 1.81: 52 Bond restraints: 19486 Sorted by residual: bond pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CA GLY U 59 " pdb=" C GLY U 59 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.48e+00 bond pdb=" N GLY D 53 " pdb=" CA GLY D 53 " ideal model delta sigma weight residual 1.442 1.450 -0.009 7.70e-03 1.69e+04 1.26e+00 bond pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CA GLU U 60 " pdb=" C GLU U 60 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.19e+00 ... (remaining 19481 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.09: 1670 105.09 - 112.31: 10822 112.31 - 119.53: 5950 119.53 - 126.75: 8424 126.75 - 133.97: 1157 Bond angle restraints: 28023 Sorted by residual: angle pdb=" CA GLY D 53 " pdb=" C GLY D 53 " pdb=" N ILE D 54 " ideal model delta sigma weight residual 114.65 118.04 -3.39 9.20e-01 1.18e+00 1.36e+01 angle pdb=" CB LYS C 74 " pdb=" CG LYS C 74 " pdb=" CD LYS C 74 " ideal model delta sigma weight residual 111.30 118.42 -7.12 2.30e+00 1.89e-01 9.57e+00 angle pdb=" C3' DC I 72 " pdb=" C2' DC I 72 " pdb=" C1' DC I 72 " ideal model delta sigma weight residual 101.60 97.87 3.73 1.50e+00 4.44e-01 6.17e+00 angle pdb=" C TYR M 69 " pdb=" N ALA M 70 " pdb=" CA ALA M 70 " ideal model delta sigma weight residual 121.54 126.04 -4.50 1.91e+00 2.74e-01 5.56e+00 angle pdb=" N ARG B 23 " pdb=" CA ARG B 23 " pdb=" C ARG B 23 " ideal model delta sigma weight residual 110.80 115.67 -4.87 2.13e+00 2.20e-01 5.23e+00 ... (remaining 28018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 8763 35.60 - 71.19: 1849 71.19 - 106.79: 24 106.79 - 142.38: 0 142.38 - 177.98: 2 Dihedral angle restraints: 10638 sinusoidal: 6875 harmonic: 3763 Sorted by residual: dihedral pdb=" C4' DT J 153 " pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sinusoidal sigma weight residual 220.00 42.02 177.98 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N ARG A 83 " pdb=" CA ARG A 83 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C4' DG J 119 " pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " pdb=" P DG J 120 " ideal model delta sinusoidal sigma weight residual 220.00 70.16 149.84 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 10635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2015 0.031 - 0.062: 855 0.062 - 0.093: 194 0.093 - 0.125: 84 0.125 - 0.156: 6 Chirality restraints: 3154 Sorted by residual: chirality pdb=" CB THR M 102 " pdb=" CA THR M 102 " pdb=" OG1 THR M 102 " pdb=" CG2 THR M 102 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA ILE N 67 " pdb=" N ILE N 67 " pdb=" C ILE N 67 " pdb=" CB ILE N 67 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE M 94 " pdb=" N ILE M 94 " pdb=" C ILE M 94 " pdb=" CB ILE M 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 3151 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET M 169 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO M 170 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO M 170 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 170 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO D 103 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO H 103 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.023 5.00e-02 4.00e+02 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 861 2.71 - 3.25: 16531 3.25 - 3.80: 35102 3.80 - 4.35: 44424 4.35 - 4.90: 64273 Nonbonded interactions: 161191 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.158 2.440 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG M 251 " model vdw 2.204 2.520 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.205 2.520 nonbonded pdb=" OE1 GLN M 184 " pdb=" NE1 TRP M 196 " model vdw 2.236 2.520 nonbonded pdb=" OE1 GLU D 71 " pdb=" NZ LYS F 91 " model vdw 2.251 2.520 ... (remaining 161186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 4.510 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 54.400 Find NCS groups from input model: 0.730 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19486 Z= 0.248 Angle : 0.621 7.116 28023 Z= 0.377 Chirality : 0.037 0.156 3154 Planarity : 0.004 0.057 2171 Dihedral : 26.716 177.979 8228 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % 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: 0.98 (0.23), residues: 1272 helix: 1.53 (0.21), residues: 592 sheet: 0.23 (0.33), residues: 238 loop : -0.18 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 196 HIS 0.005 0.001 HIS M 110 PHE 0.013 0.002 PHE C 25 TYR 0.022 0.002 TYR G 50 ARG 0.009 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 71 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7953 (ttm-80) REVERT: D 59 MET cc_start: 0.8102 (tpt) cc_final: 0.7660 (tpt) REVERT: D 86 ARG cc_start: 0.8279 (mtp85) cc_final: 0.8036 (mmt-90) REVERT: E 60 LEU cc_start: 0.8527 (mt) cc_final: 0.8224 (mt) REVERT: F 55 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8464 (mtm-85) REVERT: F 79 LYS cc_start: 0.8084 (mttp) cc_final: 0.7858 (mttp) REVERT: F 85 ASP cc_start: 0.7515 (m-30) cc_final: 0.7300 (m-30) REVERT: G 73 ASN cc_start: 0.7897 (t0) cc_final: 0.7286 (t0) REVERT: H 83 TYR cc_start: 0.8482 (m-10) cc_final: 0.8188 (m-10) REVERT: M 68 TYR cc_start: 0.8352 (p90) cc_final: 0.8068 (p90) REVERT: M 155 GLN cc_start: 0.7442 (tt0) cc_final: 0.7188 (tt0) REVERT: U 70 TYR cc_start: 0.8753 (t80) cc_final: 0.8436 (t80) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.3788 time to fit residues: 145.7339 Evaluate side-chains 237 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 104 GLN E 125 GLN F 25 ASN F 27 GLN F 93 GLN G 24 GLN N 95 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19486 Z= 0.185 Angle : 0.554 6.525 28023 Z= 0.331 Chirality : 0.035 0.151 3154 Planarity : 0.004 0.057 2171 Dihedral : 29.681 178.985 5718 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.63 % Allowed : 6.62 % Favored : 91.75 % 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: 1.53 (0.23), residues: 1272 helix: 2.17 (0.21), residues: 592 sheet: 0.67 (0.35), residues: 214 loop : -0.30 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 196 HIS 0.003 0.001 HIS A 113 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.001 TYR G 50 ARG 0.013 0.000 ARG U 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 250 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7215 (mmm) cc_final: 0.6983 (mmt) REVERT: A 119 ILE cc_start: 0.9078 (pt) cc_final: 0.8860 (pt) REVERT: B 26 ILE cc_start: 0.7879 (tp) cc_final: 0.7596 (tp) REVERT: D 72 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8213 (mtm180) REVERT: D 86 ARG cc_start: 0.8319 (mtp85) cc_final: 0.8088 (mmt-90) REVERT: F 85 ASP cc_start: 0.7458 (m-30) cc_final: 0.7223 (m-30) REVERT: G 73 ASN cc_start: 0.7985 (t0) cc_final: 0.7369 (t0) REVERT: H 83 TYR cc_start: 0.8710 (m-10) cc_final: 0.8362 (m-10) REVERT: H 116 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8326 (ttpt) REVERT: M 68 TYR cc_start: 0.8370 (p90) cc_final: 0.8138 (p90) REVERT: N 38 VAL cc_start: 0.8096 (t) cc_final: 0.7571 (t) outliers start: 18 outliers final: 13 residues processed: 259 average time/residue: 0.4057 time to fit residues: 145.3693 Evaluate side-chains 232 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 219 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 121 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 117 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 104 GLN D 47 GLN E 125 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19486 Z= 0.163 Angle : 0.524 5.451 28023 Z= 0.314 Chirality : 0.034 0.129 3154 Planarity : 0.004 0.049 2171 Dihedral : 29.640 179.695 5718 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.72 % Allowed : 8.34 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1272 helix: 2.52 (0.21), residues: 592 sheet: 0.82 (0.35), residues: 214 loop : -0.22 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 196 HIS 0.003 0.001 HIS N 110 PHE 0.007 0.001 PHE A 67 TYR 0.013 0.001 TYR U 70 ARG 0.005 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 240 time to evaluate : 1.421 Fit side-chains REVERT: A 119 ILE cc_start: 0.9052 (pt) cc_final: 0.8839 (pt) REVERT: B 80 THR cc_start: 0.8893 (m) cc_final: 0.8371 (t) REVERT: D 59 MET cc_start: 0.8006 (tpt) cc_final: 0.7423 (tpt) REVERT: G 73 ASN cc_start: 0.7998 (t0) cc_final: 0.7421 (t0) REVERT: H 83 TYR cc_start: 0.8663 (m-10) cc_final: 0.8348 (m-10) REVERT: M 195 GLU cc_start: 0.7808 (tt0) cc_final: 0.7483 (tt0) REVERT: N 98 GLU cc_start: 0.7657 (mp0) cc_final: 0.7249 (pm20) REVERT: U 83 ASN cc_start: 0.8012 (p0) cc_final: 0.7779 (p0) REVERT: U 114 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7592 (ttpp) outliers start: 19 outliers final: 12 residues processed: 248 average time/residue: 0.3889 time to fit residues: 133.4409 Evaluate side-chains 223 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN D 47 GLN E 68 GLN E 125 GLN F 75 HIS M 110 HIS ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN U 103 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19486 Z= 0.217 Angle : 0.534 5.387 28023 Z= 0.318 Chirality : 0.035 0.150 3154 Planarity : 0.004 0.049 2171 Dihedral : 29.775 177.600 5718 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.09 % Allowed : 9.79 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1272 helix: 2.48 (0.21), residues: 592 sheet: 0.57 (0.33), residues: 240 loop : -0.20 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 185 HIS 0.004 0.001 HIS M 110 PHE 0.010 0.001 PHE C 25 TYR 0.013 0.001 TYR M 199 ARG 0.006 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 1.413 Fit side-chains REVERT: A 119 ILE cc_start: 0.9114 (pt) cc_final: 0.8886 (pt) REVERT: B 26 ILE cc_start: 0.7827 (tp) cc_final: 0.7571 (tp) REVERT: C 15 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7747 (mtpp) REVERT: C 64 GLU cc_start: 0.7345 (tt0) cc_final: 0.7059 (tt0) REVERT: E 41 TYR cc_start: 0.8722 (m-80) cc_final: 0.8431 (m-80) REVERT: G 73 ASN cc_start: 0.8076 (t0) cc_final: 0.7498 (t0) REVERT: H 83 TYR cc_start: 0.8633 (m-10) cc_final: 0.8332 (m-10) REVERT: M 68 TYR cc_start: 0.8334 (p90) cc_final: 0.8096 (p90) REVERT: N 23 MET cc_start: 0.7256 (mmm) cc_final: 0.6831 (mtp) REVERT: U 114 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7674 (ttpp) outliers start: 23 outliers final: 19 residues processed: 238 average time/residue: 0.3959 time to fit residues: 130.3953 Evaluate side-chains 227 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 208 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 132 optimal weight: 0.0270 chunk 107 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19486 Z= 0.213 Angle : 0.529 6.616 28023 Z= 0.315 Chirality : 0.034 0.143 3154 Planarity : 0.004 0.049 2171 Dihedral : 29.713 176.338 5718 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.99 % Allowed : 10.61 % Favored : 87.40 % 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: 1.82 (0.24), residues: 1272 helix: 2.52 (0.21), residues: 592 sheet: 0.48 (0.33), residues: 240 loop : -0.17 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 185 HIS 0.002 0.001 HIS D 49 PHE 0.009 0.001 PHE C 25 TYR 0.022 0.001 TYR U 70 ARG 0.007 0.000 ARG U 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 1.401 Fit side-chains REVERT: A 119 ILE cc_start: 0.9125 (pt) cc_final: 0.8905 (pt) REVERT: B 26 ILE cc_start: 0.7883 (tp) cc_final: 0.7632 (tp) REVERT: C 64 GLU cc_start: 0.7372 (tt0) cc_final: 0.7094 (tt0) REVERT: D 59 MET cc_start: 0.8091 (tpt) cc_final: 0.7540 (tpt) REVERT: G 73 ASN cc_start: 0.8107 (t0) cc_final: 0.7528 (t0) REVERT: H 83 TYR cc_start: 0.8580 (m-10) cc_final: 0.8266 (m-10) REVERT: M 68 TYR cc_start: 0.8306 (p90) cc_final: 0.8076 (p90) REVERT: N 23 MET cc_start: 0.7372 (mmm) cc_final: 0.6905 (mtp) REVERT: U 83 ASN cc_start: 0.8196 (p0) cc_final: 0.7959 (p0) REVERT: U 114 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7710 (ttpp) outliers start: 22 outliers final: 18 residues processed: 235 average time/residue: 0.3735 time to fit residues: 122.2742 Evaluate side-chains 229 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 30.0000 chunk 38 optimal weight: 0.0040 chunk 155 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 40.0000 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19486 Z= 0.222 Angle : 0.533 7.943 28023 Z= 0.316 Chirality : 0.034 0.138 3154 Planarity : 0.004 0.048 2171 Dihedral : 29.744 175.229 5718 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 11.42 % Favored : 86.40 % 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: 1.81 (0.24), residues: 1272 helix: 2.54 (0.21), residues: 592 sheet: 0.42 (0.33), residues: 240 loop : -0.18 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 185 HIS 0.003 0.001 HIS M 110 PHE 0.008 0.001 PHE C 25 TYR 0.013 0.001 TYR M 199 ARG 0.007 0.000 ARG U 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 216 time to evaluate : 1.541 Fit side-chains REVERT: A 90 MET cc_start: 0.7268 (mmm) cc_final: 0.7001 (mmt) REVERT: A 119 ILE cc_start: 0.9136 (pt) cc_final: 0.8915 (pt) REVERT: B 26 ILE cc_start: 0.7916 (tp) cc_final: 0.7663 (tp) REVERT: C 64 GLU cc_start: 0.7412 (tt0) cc_final: 0.7147 (tt0) REVERT: E 41 TYR cc_start: 0.8743 (m-80) cc_final: 0.8495 (m-80) REVERT: G 73 ASN cc_start: 0.8109 (t0) cc_final: 0.7578 (t0) REVERT: H 83 TYR cc_start: 0.8440 (m-10) cc_final: 0.8134 (m-10) REVERT: N 23 MET cc_start: 0.7458 (mmm) cc_final: 0.6898 (mtp) REVERT: N 216 LYS cc_start: 0.8065 (tppt) cc_final: 0.7790 (tptm) outliers start: 24 outliers final: 20 residues processed: 230 average time/residue: 0.3890 time to fit residues: 124.4534 Evaluate side-chains 227 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19486 Z= 0.243 Angle : 0.542 7.101 28023 Z= 0.320 Chirality : 0.035 0.142 3154 Planarity : 0.004 0.048 2171 Dihedral : 29.793 173.813 5718 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.18 % Allowed : 12.24 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.24), residues: 1272 helix: 2.48 (0.21), residues: 592 sheet: 0.25 (0.32), residues: 250 loop : -0.11 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 185 HIS 0.003 0.001 HIS D 49 PHE 0.010 0.001 PHE C 25 TYR 0.017 0.001 TYR U 70 ARG 0.006 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7266 (mmm) cc_final: 0.7011 (mmt) REVERT: A 119 ILE cc_start: 0.9160 (pt) cc_final: 0.8944 (pt) REVERT: B 26 ILE cc_start: 0.8015 (tp) cc_final: 0.7791 (tp) REVERT: D 59 MET cc_start: 0.8130 (tpt) cc_final: 0.7569 (tpt) REVERT: G 73 ASN cc_start: 0.8123 (t0) cc_final: 0.7591 (t0) REVERT: H 83 TYR cc_start: 0.8464 (m-10) cc_final: 0.8146 (m-10) REVERT: M 162 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6326 (pm20) REVERT: N 23 MET cc_start: 0.7477 (mmm) cc_final: 0.7033 (mmm) REVERT: N 216 LYS cc_start: 0.8081 (tppt) cc_final: 0.7755 (tptm) REVERT: U 83 ASN cc_start: 0.8092 (p0) cc_final: 0.7882 (p0) outliers start: 24 outliers final: 20 residues processed: 230 average time/residue: 0.4036 time to fit residues: 128.0509 Evaluate side-chains 233 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19486 Z= 0.235 Angle : 0.540 7.038 28023 Z= 0.319 Chirality : 0.035 0.139 3154 Planarity : 0.004 0.047 2171 Dihedral : 29.790 173.798 5718 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.45 % Allowed : 12.33 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1272 helix: 2.49 (0.21), residues: 592 sheet: 0.28 (0.32), residues: 250 loop : -0.13 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 185 HIS 0.003 0.001 HIS D 49 PHE 0.009 0.001 PHE G 25 TYR 0.014 0.001 TYR M 199 ARG 0.008 0.000 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 1.479 Fit side-chains REVERT: A 79 LYS cc_start: 0.8334 (ttpp) cc_final: 0.8050 (ttpt) REVERT: A 90 MET cc_start: 0.7252 (mmm) cc_final: 0.6999 (mmt) REVERT: A 119 ILE cc_start: 0.9157 (pt) cc_final: 0.8939 (pt) REVERT: B 26 ILE cc_start: 0.8013 (tp) cc_final: 0.7776 (tp) REVERT: D 59 MET cc_start: 0.8130 (tpt) cc_final: 0.7544 (tpt) REVERT: G 73 ASN cc_start: 0.8102 (t0) cc_final: 0.7617 (t0) REVERT: M 68 TYR cc_start: 0.8320 (p90) cc_final: 0.8112 (p90) REVERT: M 162 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: N 23 MET cc_start: 0.7460 (mmm) cc_final: 0.7017 (mmm) REVERT: N 49 ARG cc_start: 0.8333 (mtm110) cc_final: 0.8131 (mtm180) REVERT: N 216 LYS cc_start: 0.8085 (tppt) cc_final: 0.7755 (tptm) outliers start: 27 outliers final: 23 residues processed: 230 average time/residue: 0.3862 time to fit residues: 123.3577 Evaluate side-chains 235 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 4.9990 chunk 148 optimal weight: 0.0770 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19486 Z= 0.163 Angle : 0.526 6.255 28023 Z= 0.314 Chirality : 0.034 0.133 3154 Planarity : 0.004 0.047 2171 Dihedral : 29.784 173.867 5718 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.81 % Allowed : 13.33 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1272 helix: 2.60 (0.21), residues: 592 sheet: 0.32 (0.32), residues: 250 loop : -0.10 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 185 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE A 67 TYR 0.022 0.001 TYR U 70 ARG 0.006 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 211 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8107 (ttpt) REVERT: A 90 MET cc_start: 0.7225 (mmm) cc_final: 0.6976 (mmt) REVERT: A 119 ILE cc_start: 0.9127 (pt) cc_final: 0.8908 (pt) REVERT: B 26 ILE cc_start: 0.7944 (tp) cc_final: 0.7711 (tp) REVERT: D 59 MET cc_start: 0.8045 (tpt) cc_final: 0.7517 (tpt) REVERT: G 73 ASN cc_start: 0.8081 (t0) cc_final: 0.7604 (t0) REVERT: M 68 TYR cc_start: 0.8298 (p90) cc_final: 0.8086 (p90) REVERT: M 162 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6294 (pm20) REVERT: N 23 MET cc_start: 0.7327 (mmm) cc_final: 0.7110 (mmm) REVERT: N 216 LYS cc_start: 0.8060 (tppt) cc_final: 0.7721 (tptm) outliers start: 20 outliers final: 16 residues processed: 222 average time/residue: 0.3987 time to fit residues: 122.1502 Evaluate side-chains 226 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 40.0000 chunk 106 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 147 optimal weight: 0.0070 chunk 127 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19486 Z= 0.271 Angle : 0.553 7.391 28023 Z= 0.326 Chirality : 0.035 0.139 3154 Planarity : 0.004 0.047 2171 Dihedral : 29.829 173.295 5718 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.63 % Allowed : 13.51 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1272 helix: 2.43 (0.21), residues: 592 sheet: 0.32 (0.33), residues: 250 loop : -0.17 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 185 HIS 0.004 0.001 HIS D 49 PHE 0.011 0.001 PHE C 25 TYR 0.018 0.002 TYR H 83 ARG 0.007 0.000 ARG M 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 216 time to evaluate : 1.426 Fit side-chains REVERT: A 79 LYS cc_start: 0.8390 (ttpp) cc_final: 0.8126 (ttpt) REVERT: A 119 ILE cc_start: 0.9169 (pt) cc_final: 0.8954 (pt) REVERT: B 26 ILE cc_start: 0.8042 (tp) cc_final: 0.7807 (tp) REVERT: G 73 ASN cc_start: 0.8183 (t0) cc_final: 0.7624 (t0) REVERT: M 162 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: N 23 MET cc_start: 0.7434 (mmm) cc_final: 0.6960 (mtp) REVERT: N 216 LYS cc_start: 0.8086 (tppt) cc_final: 0.7738 (tptm) outliers start: 18 outliers final: 17 residues processed: 227 average time/residue: 0.4047 time to fit residues: 128.9171 Evaluate side-chains 230 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 112 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.153861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109134 restraints weight = 26041.267| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.27 r_work: 0.3235 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19486 Z= 0.183 Angle : 0.533 6.044 28023 Z= 0.318 Chirality : 0.034 0.136 3154 Planarity : 0.004 0.046 2171 Dihedral : 29.834 173.319 5718 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.90 % Allowed : 13.60 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1272 helix: 2.48 (0.21), residues: 592 sheet: 0.34 (0.33), residues: 240 loop : -0.11 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 185 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE U 113 TYR 0.028 0.002 TYR B 88 ARG 0.008 0.000 ARG E 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.43 seconds wall clock time: 69 minutes 49.51 seconds (4189.51 seconds total)