Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 16:22:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/04_2023/7k60_22685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/04_2023/7k60_22685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/04_2023/7k60_22685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/04_2023/7k60_22685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/04_2023/7k60_22685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/04_2023/7k60_22685.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 52": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M ARG 37": "NH1" <-> "NH2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 75": "OD1" <-> "OD2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 36": "OE1" <-> "OE2" Residue "N ARG 37": "NH1" <-> "NH2" Residue "N TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "N ASP 89": "OD1" <-> "OD2" Residue "N ASP 101": "OD1" <-> "OD2" Residue "N GLU 159": "OE1" <-> "OE2" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 211": "OE1" <-> "OE2" Residue "N ASP 222": "OD1" <-> "OD2" Residue "N TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 239": "OD1" <-> "OD2" Residue "U TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 53": "OE1" <-> "OE2" 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-1.21rc1-4938/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: 9.23, per 1000 atoms: 0.50 Number of scatterers: 18330 At special positions: 0 Unit cell: (136.68, 123.28, 198.32, 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: 9.67 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 48.6% alpha, 21.0% beta 197 base pairs and 330 stacking pairs defined. Time for finding SS restraints: 8.21 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.723A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.551A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) 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: 3.611A 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 removed outlier: 3.538A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.153A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.534A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.614A 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: 3.669A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.189A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.762A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.640A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.906A 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: 3.884A 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: 6.758A 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: 7.365A 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: 6.559A 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: 6.726A 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: 7.352A 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: 3.786A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.653A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.507A 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 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: 6.345A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR M 181 " --> pdb=" O TYR M 201 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR M 201 " --> pdb=" O TYR M 181 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS M 208 " --> pdb=" O TYR M 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.345A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 24 removed outlier: 3.839A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.608A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.458A 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: 7.932A pdb=" N TYR N 181 " --> pdb=" O TYR N 201 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR N 201 " --> pdb=" O TYR N 181 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.866A 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: 3.955A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.805A pdb=" N SER U 112 " --> pdb=" O VAL U 104 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 330 stacking parallelities Total time for adding SS restraints: 7.76 Time building geometry restraints manager: 10.17 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: 2773 1.33 - 1.45: 6782 1.45 - 1.57: 9093 1.57 - 1.69: 786 1.69 - 1.81: 52 Bond restraints: 19486 Sorted by residual: bond pdb=" C PRO M 114 " pdb=" O PRO M 114 " ideal model delta sigma weight residual 1.235 1.223 0.012 7.90e-03 1.60e+04 2.47e+00 bond pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CA PRO M 114 " pdb=" C PRO M 114 " ideal model delta sigma weight residual 1.521 1.533 -0.013 9.30e-03 1.16e+04 1.82e+00 bond pdb=" CZ ARG D 31 " pdb=" NH2 ARG D 31 " ideal model delta sigma weight residual 1.330 1.314 0.016 1.30e-02 5.92e+03 1.48e+00 bond pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 19481 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.26: 1730 105.26 - 112.44: 10791 112.44 - 119.62: 6111 119.62 - 126.80: 8242 126.80 - 133.98: 1149 Bond angle restraints: 28023 Sorted by residual: angle pdb=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.97 125.40 -4.43 1.48e+00 4.57e-01 8.98e+00 angle pdb=" C TYR N 69 " pdb=" N ALA N 70 " pdb=" CA ALA N 70 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.36e+00 angle pdb=" C GLN N 25 " pdb=" N SER N 26 " pdb=" CA SER N 26 " ideal model delta sigma weight residual 119.78 122.81 -3.03 1.24e+00 6.50e-01 5.99e+00 angle pdb=" CA TYR U 90 " pdb=" CB TYR U 90 " pdb=" CG TYR U 90 " ideal model delta sigma weight residual 113.90 118.26 -4.36 1.80e+00 3.09e-01 5.86e+00 angle pdb=" C3' DC J 97 " pdb=" C2' DC J 97 " pdb=" C1' DC J 97 " ideal model delta sigma weight residual 101.60 98.07 3.53 1.50e+00 4.44e-01 5.52e+00 ... (remaining 28018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 8412 34.38 - 68.75: 1872 68.75 - 103.13: 28 103.13 - 137.51: 0 137.51 - 171.89: 2 Dihedral angle restraints: 10314 sinusoidal: 6551 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 48.11 171.89 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 119 " pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " pdb=" P DG J 120 " ideal model delta sinusoidal sigma weight residual 220.00 74.51 145.49 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA TYR N 106 " pdb=" C TYR N 106 " pdb=" N CYS N 107 " pdb=" CA CYS N 107 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 10311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2316 0.038 - 0.076: 664 0.076 - 0.114: 145 0.114 - 0.152: 26 0.152 - 0.189: 3 Chirality restraints: 3154 Sorted by residual: chirality pdb=" CB THR N 177 " pdb=" CA THR N 177 " pdb=" OG1 THR N 177 " pdb=" CG2 THR N 177 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CB THR M 177 " pdb=" CA THR M 177 " pdb=" OG1 THR M 177 " pdb=" CG2 THR M 177 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA LYS F 31 " pdb=" N LYS F 31 " pdb=" C LYS F 31 " pdb=" CB LYS F 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 3151 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 40 " 0.014 2.00e-02 2.50e+03 1.69e-02 5.72e+00 pdb=" CG TYR D 40 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR D 40 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 40 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 40 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 40 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 40 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 201 " -0.017 2.00e-02 2.50e+03 1.59e-02 5.08e+00 pdb=" CG TYR N 201 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR N 201 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR N 201 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR N 201 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR N 201 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR N 201 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR N 201 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 66 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.028 5.00e-02 4.00e+02 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1085 2.72 - 3.27: 16996 3.27 - 3.81: 35484 3.81 - 4.36: 43449 4.36 - 4.90: 63293 Nonbonded interactions: 160307 Sorted by model distance: nonbonded pdb=" NH2 ARG N 80 " pdb=" O ASN N 96 " model vdw 2.175 2.520 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.177 2.440 nonbonded pdb=" OH TYR M 55 " pdb=" OG1 THR M 255 " model vdw 2.182 2.440 nonbonded pdb=" O ASN G 73 " pdb=" ND2 ASN G 73 " model vdw 2.192 2.520 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.219 2.440 ... (remaining 160302 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 5.300 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 56.750 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 0.052 19486 Z= 0.228 Angle : 0.642 8.767 28023 Z= 0.390 Chirality : 0.038 0.189 3154 Planarity : 0.004 0.050 2171 Dihedral : 26.720 171.886 7904 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.09 % 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: 0.43 (0.23), residues: 1272 helix: 1.02 (0.20), residues: 590 sheet: 0.43 (0.34), residues: 238 loop : -0.68 (0.28), residues: 444 *********************** 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 244 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.3615 time to fit residues: 127.1179 Evaluate side-chains 188 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8855 ------------------------------------------------------------------------------- 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: 5.9990 chunk 122 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN U 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 19486 Z= 0.282 Angle : 0.624 9.126 28023 Z= 0.366 Chirality : 0.039 0.170 3154 Planarity : 0.005 0.048 2171 Dihedral : 30.569 174.092 5394 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.36 % 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: 0.60 (0.23), residues: 1272 helix: 1.11 (0.20), residues: 590 sheet: 0.66 (0.35), residues: 218 loop : -0.58 (0.27), residues: 464 *********************** 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 216 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.525 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 209 average time/residue: 0.3431 time to fit residues: 104.3521 Evaluate side-chains 195 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1698 time to fit residues: 5.5481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN N 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 19486 Z= 0.319 Angle : 0.635 10.448 28023 Z= 0.371 Chirality : 0.039 0.162 3154 Planarity : 0.005 0.046 2171 Dihedral : 30.761 174.577 5394 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.45 % 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: 0.32 (0.23), residues: 1272 helix: 0.86 (0.20), residues: 588 sheet: 0.40 (0.34), residues: 230 loop : -0.62 (0.28), residues: 454 *********************** 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 210 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 1.604 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 204 average time/residue: 0.3520 time to fit residues: 104.5606 Evaluate side-chains 190 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1689 time to fit residues: 5.9079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.5980 chunk 110 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2302 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= 0.226 Angle : 0.579 9.744 28023 Z= 0.342 Chirality : 0.036 0.146 3154 Planarity : 0.004 0.043 2171 Dihedral : 30.552 174.164 5394 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.45 % 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: 0.67 (0.23), residues: 1272 helix: 1.26 (0.21), residues: 590 sheet: 0.42 (0.33), residues: 230 loop : -0.53 (0.28), residues: 452 *********************** 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 206 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 201 average time/residue: 0.3577 time to fit residues: 103.8428 Evaluate side-chains 183 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1652 time to fit residues: 4.1170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19486 Z= 0.217 Angle : 0.579 11.317 28023 Z= 0.339 Chirality : 0.035 0.152 3154 Planarity : 0.004 0.043 2171 Dihedral : 30.476 176.016 5394 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.27 % 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: 0.82 (0.23), residues: 1272 helix: 1.43 (0.21), residues: 590 sheet: 0.51 (0.34), residues: 230 loop : -0.54 (0.28), residues: 452 *********************** 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 201 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 194 average time/residue: 0.3564 time to fit residues: 100.6594 Evaluate side-chains 182 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1725 time to fit residues: 4.1808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 19486 Z= 0.285 Angle : 0.617 11.808 28023 Z= 0.358 Chirality : 0.037 0.176 3154 Planarity : 0.004 0.042 2171 Dihedral : 30.629 177.271 5394 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.90 % 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: 0.50 (0.23), residues: 1272 helix: 1.13 (0.20), residues: 590 sheet: 0.47 (0.33), residues: 238 loop : -0.74 (0.28), residues: 444 *********************** 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 210 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 202 average time/residue: 0.3572 time to fit residues: 104.7486 Evaluate side-chains 187 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1987 time to fit residues: 6.3118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN N 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2933 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= 0.232 Angle : 0.586 12.565 28023 Z= 0.342 Chirality : 0.036 0.160 3154 Planarity : 0.004 0.040 2171 Dihedral : 30.493 176.670 5394 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1272 helix: 1.35 (0.21), residues: 590 sheet: 0.42 (0.33), residues: 238 loop : -0.74 (0.28), residues: 444 *********************** 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 191 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 187 average time/residue: 0.3387 time to fit residues: 92.8899 Evaluate side-chains 181 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1672 time to fit residues: 3.1128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 141 optimal weight: 0.0270 chunk 148 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN M 31 HIS N 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19486 Z= 0.174 Angle : 0.565 12.990 28023 Z= 0.331 Chirality : 0.034 0.157 3154 Planarity : 0.004 0.041 2171 Dihedral : 30.261 176.895 5394 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.91 % 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: 1.09 (0.23), residues: 1272 helix: 1.80 (0.21), residues: 592 sheet: 0.46 (0.33), residues: 240 loop : -0.57 (0.29), residues: 440 *********************** 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 206 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 204 average time/residue: 0.3402 time to fit residues: 101.9398 Evaluate side-chains 188 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1840 time to fit residues: 3.6310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.0770 chunk 148 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 136 optimal weight: 0.0670 chunk 94 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.4280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN N 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3220 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= 0.235 Angle : 0.605 14.339 28023 Z= 0.347 Chirality : 0.036 0.207 3154 Planarity : 0.004 0.041 2171 Dihedral : 30.400 179.111 5394 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.82 % 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: 0.88 (0.23), residues: 1272 helix: 1.55 (0.21), residues: 592 sheet: 0.47 (0.33), residues: 238 loop : -0.62 (0.29), residues: 442 *********************** 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 185 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 181 average time/residue: 0.3322 time to fit residues: 88.5771 Evaluate side-chains 180 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1722 time to fit residues: 3.6993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 chunk 160 optimal weight: 0.0020 chunk 147 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19486 Z= 0.205 Angle : 0.589 13.700 28023 Z= 0.340 Chirality : 0.035 0.185 3154 Planarity : 0.004 0.040 2171 Dihedral : 30.309 178.478 5394 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.09 % 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: 1.00 (0.23), residues: 1272 helix: 1.70 (0.21), residues: 590 sheet: 0.55 (0.33), residues: 238 loop : -0.63 (0.29), residues: 444 ********************** 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 181 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.3426 time to fit residues: 91.5946 Evaluate side-chains 175 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1720 time to fit residues: 2.2069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 GLN N 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.168559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.123314 restraints weight = 29828.250| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.68 r_work: 0.3463 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19486 Z= 0.191 Angle : 0.581 13.620 28023 Z= 0.335 Chirality : 0.035 0.154 3154 Planarity : 0.004 0.040 2171 Dihedral : 30.255 178.902 5394 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.45 % 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: 1.07 (0.23), residues: 1272 helix: 1.77 (0.21), residues: 592 sheet: 0.52 (0.33), residues: 238 loop : -0.60 (0.29), residues: 442 =============================================================================== Job complete usr+sys time: 4002.29 seconds wall clock time: 73 minutes 1.23 seconds (4381.23 seconds total)