Starting phenix.real_space_refine on Mon Mar 18 09:32:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/03_2024/7k60_22685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/03_2024/7k60_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_22685/03_2024/7k60_22685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/03_2024/7k60_22685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/03_2024/7k60_22685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k60_22685/03_2024/7k60_22685.pdb" } resolution = 3.12 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 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: 0.03s 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: 8.96, per 1000 atoms: 0.49 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: 9.28 Conformation dependent library (CDL) restraints added in 2.0 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: 8.12 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: 7.08 Time building geometry restraints manager: 9.86 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: 8722 34.38 - 68.75: 1886 68.75 - 103.13: 28 103.13 - 137.51: 0 137.51 - 171.89: 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 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 10635 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: 0.010 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 4.820 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 55.590 Find NCS groups from input model: 0.710 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.210 ------------------------------------------------------------------------------- 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 : 26.554 171.886 8228 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 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP M 60 HIS 0.005 0.002 HIS E 113 PHE 0.013 0.002 PHE C 25 TYR 0.041 0.002 TYR D 40 ARG 0.013 0.001 ARG N 37 *********************** 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 : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7284 (mmp) cc_final: 0.7022 (mmp) REVERT: A 94 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6769 (mm-30) REVERT: B 95 ARG cc_start: 0.7854 (mmt-90) cc_final: 0.7628 (mpt180) REVERT: D 59 MET cc_start: 0.7018 (tpp) cc_final: 0.6098 (tpt) REVERT: D 67 ASN cc_start: 0.8173 (m-40) cc_final: 0.7951 (m110) REVERT: G 90 ASP cc_start: 0.6586 (t0) cc_final: 0.6305 (t0) REVERT: N 229 TYR cc_start: 0.6648 (m-80) cc_final: 0.6434 (m-80) REVERT: N 238 GLU cc_start: 0.7589 (tt0) cc_final: 0.7352 (pt0) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.3126 time to fit residues: 109.9986 Evaluate side-chains 188 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19486 Z= 0.282 Angle : 0.625 8.886 28023 Z= 0.367 Chirality : 0.039 0.172 3154 Planarity : 0.005 0.048 2171 Dihedral : 30.052 174.113 5718 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.36 % Allowed : 8.61 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1272 helix: 1.12 (0.20), residues: 590 sheet: 0.67 (0.35), residues: 218 loop : -0.58 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 54 HIS 0.005 0.002 HIS C 82 PHE 0.013 0.002 PHE C 25 TYR 0.024 0.002 TYR B 88 ARG 0.005 0.001 ARG F 45 *********************** 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 214 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 1.393 Fit side-chains REVERT: A 87 SER cc_start: 0.7488 (t) cc_final: 0.7241 (p) REVERT: A 94 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6817 (mm-30) REVERT: B 95 ARG cc_start: 0.7837 (mmt-90) cc_final: 0.7580 (mpt180) REVERT: C 55 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7535 (mp) REVERT: D 42 TYR cc_start: 0.7484 (t80) cc_final: 0.6809 (t80) REVERT: D 59 MET cc_start: 0.6914 (tpp) cc_final: 0.6301 (tpt) REVERT: E 50 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7171 (mt-10) REVERT: G 90 ASP cc_start: 0.6683 (t0) cc_final: 0.6459 (t0) REVERT: H 30 LYS cc_start: 0.5491 (tppt) cc_final: 0.5026 (tttp) REVERT: H 57 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8162 (mmmt) REVERT: H 59 MET cc_start: 0.7031 (tpp) cc_final: 0.6757 (tpt) REVERT: N 98 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6964 (mm-30) outliers start: 15 outliers final: 10 residues processed: 208 average time/residue: 0.3379 time to fit residues: 101.6609 Evaluate side-chains 192 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 181 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain N residue 257 ASP 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: 0.0470 chunk 121 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- 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 H 84 ASN N 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19486 Z= 0.304 Angle : 0.628 9.419 28023 Z= 0.367 Chirality : 0.038 0.154 3154 Planarity : 0.005 0.047 2171 Dihedral : 30.236 174.675 5718 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.45 % Allowed : 12.06 % Favored : 85.49 % 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: 0.35 (0.23), residues: 1272 helix: 0.89 (0.20), residues: 590 sheet: 0.36 (0.34), residues: 230 loop : -0.59 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP M 60 HIS 0.005 0.002 HIS N 110 PHE 0.015 0.002 PHE C 25 TYR 0.018 0.002 TYR B 88 ARG 0.006 0.001 ARG N 37 *********************** 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 225 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6851 (mm-30) REVERT: B 95 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7627 (mpt180) REVERT: D 40 TYR cc_start: 0.7628 (m-80) cc_final: 0.7256 (m-80) REVERT: D 59 MET cc_start: 0.6932 (tpp) cc_final: 0.6551 (tpt) REVERT: E 50 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7124 (mt-10) REVERT: M 21 ILE cc_start: 0.8175 (mp) cc_final: 0.7933 (mp) REVERT: N 20 ASP cc_start: 0.8356 (t0) cc_final: 0.8094 (t0) outliers start: 27 outliers final: 17 residues processed: 215 average time/residue: 0.3340 time to fit residues: 104.2340 Evaluate side-chains 196 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain N residue 238 GLU Chi-restraints excluded: chain N residue 245 CYS Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.0980 chunk 110 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19486 Z= 0.189 Angle : 0.564 10.814 28023 Z= 0.334 Chirality : 0.035 0.152 3154 Planarity : 0.004 0.043 2171 Dihedral : 29.925 174.216 5718 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.36 % Allowed : 13.69 % Favored : 83.95 % 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: 0.94 (0.23), residues: 1272 helix: 1.53 (0.21), residues: 590 sheet: 0.54 (0.33), residues: 230 loop : -0.48 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 60 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE C 25 TYR 0.016 0.001 TYR B 88 ARG 0.006 0.000 ARG N 37 *********************** 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 219 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6833 (mm-30) REVERT: B 95 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7541 (mpt180) REVERT: D 42 TYR cc_start: 0.7467 (t80) cc_final: 0.6763 (t80) REVERT: D 62 MET cc_start: 0.8229 (mmm) cc_final: 0.8012 (mmm) REVERT: E 50 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7153 (mt-10) REVERT: H 59 MET cc_start: 0.7002 (tpp) cc_final: 0.6586 (tpt) REVERT: M 21 ILE cc_start: 0.8161 (mp) cc_final: 0.7865 (mp) REVERT: M 36 GLU cc_start: 0.7467 (pt0) cc_final: 0.7232 (pt0) outliers start: 26 outliers final: 14 residues processed: 207 average time/residue: 0.3451 time to fit residues: 102.6998 Evaluate side-chains 189 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 245 CYS 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: 1.9990 chunk 64 optimal weight: 0.4980 chunk 132 optimal weight: 0.0370 chunk 107 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 1.2462 ------------------------------------------------------------------------------- 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: 0.7184 moved from start: 0.2571 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= 0.214 Angle : 0.577 11.176 28023 Z= 0.338 Chirality : 0.035 0.156 3154 Planarity : 0.004 0.042 2171 Dihedral : 29.901 176.303 5718 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.27 % Allowed : 15.05 % Favored : 82.68 % 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: 0.94 (0.23), residues: 1272 helix: 1.56 (0.21), residues: 590 sheet: 0.56 (0.33), residues: 240 loop : -0.55 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 60 HIS 0.003 0.001 HIS N 110 PHE 0.008 0.001 PHE F 61 TYR 0.027 0.001 TYR D 40 ARG 0.006 0.000 ARG N 37 *********************** 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 211 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.7328 (t) cc_final: 0.7109 (p) REVERT: A 94 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6858 (mm-30) REVERT: B 95 ARG cc_start: 0.7810 (mmt-90) cc_final: 0.7531 (mpt180) REVERT: E 50 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7148 (mt-10) REVERT: E 112 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8508 (mp) REVERT: H 59 MET cc_start: 0.7012 (tpp) cc_final: 0.6617 (tpt) REVERT: M 21 ILE cc_start: 0.8176 (mp) cc_final: 0.7907 (mp) outliers start: 25 outliers final: 17 residues processed: 204 average time/residue: 0.3369 time to fit residues: 100.1975 Evaluate side-chains 188 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 245 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.7251 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19486 Z= 0.318 Angle : 0.637 12.500 28023 Z= 0.367 Chirality : 0.038 0.176 3154 Planarity : 0.005 0.043 2171 Dihedral : 30.172 177.062 5718 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.17 % Allowed : 15.23 % Favored : 81.60 % 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: 0.42 (0.23), residues: 1272 helix: 1.02 (0.20), residues: 590 sheet: 0.48 (0.33), residues: 238 loop : -0.74 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 60 HIS 0.006 0.001 HIS N 110 PHE 0.015 0.002 PHE C 25 TYR 0.026 0.002 TYR D 40 ARG 0.008 0.001 ARG N 37 *********************** 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 216 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8451 (mt) REVERT: A 94 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6849 (mm-30) REVERT: B 95 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7548 (mpt180) REVERT: E 112 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8802 (mp) outliers start: 35 outliers final: 26 residues processed: 206 average time/residue: 0.3235 time to fit residues: 97.9245 Evaluate side-chains 201 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 245 CYS Chi-restraints excluded: chain N residue 257 ASP 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: 2.9990 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.7271 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19486 Z= 0.341 Angle : 0.650 11.872 28023 Z= 0.375 Chirality : 0.039 0.169 3154 Planarity : 0.005 0.042 2171 Dihedral : 30.266 176.878 5718 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.72 % Allowed : 15.23 % Favored : 81.05 % 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: 0.08 (0.22), residues: 1272 helix: 0.80 (0.20), residues: 588 sheet: 0.20 (0.33), residues: 228 loop : -0.92 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP M 60 HIS 0.007 0.001 HIS N 110 PHE 0.016 0.002 PHE C 25 TYR 0.027 0.002 TYR D 40 ARG 0.006 0.001 ARG N 37 *********************** 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 224 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 94 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6805 (mm-30) REVERT: B 95 ARG cc_start: 0.7861 (mmt-90) cc_final: 0.7530 (mpt180) REVERT: E 50 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7145 (mt-10) REVERT: E 112 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8788 (mp) outliers start: 41 outliers final: 29 residues processed: 206 average time/residue: 0.3305 time to fit residues: 99.7953 Evaluate side-chains 208 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 30 MET Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 245 CYS Chi-restraints excluded: chain N residue 257 ASP 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: 0.5980 chunk 30 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 N 95 ASN N 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19486 Z= 0.197 Angle : 0.579 13.077 28023 Z= 0.339 Chirality : 0.035 0.153 3154 Planarity : 0.004 0.041 2171 Dihedral : 29.928 175.925 5718 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.08 % Allowed : 16.59 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1272 helix: 1.45 (0.21), residues: 590 sheet: 0.33 (0.33), residues: 238 loop : -0.74 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 60 HIS 0.003 0.001 HIS B 75 PHE 0.012 0.001 PHE E 67 TYR 0.026 0.001 TYR D 40 ARG 0.006 0.000 ARG N 80 *********************** 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 218 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8401 (mt) REVERT: B 95 ARG cc_start: 0.7766 (mmt-90) cc_final: 0.7476 (mpt180) REVERT: E 50 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7165 (mt-10) REVERT: E 112 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8596 (mp) outliers start: 34 outliers final: 27 residues processed: 210 average time/residue: 0.3199 time to fit residues: 99.6918 Evaluate side-chains 207 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 30 MET Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 245 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.0060 chunk 148 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 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 31 HIS G 73 ASN N 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3260 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= 0.246 Angle : 0.603 12.836 28023 Z= 0.351 Chirality : 0.036 0.153 3154 Planarity : 0.004 0.041 2171 Dihedral : 29.991 177.188 5718 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.99 % Allowed : 16.59 % Favored : 80.42 % 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: 0.65 (0.23), residues: 1272 helix: 1.39 (0.21), residues: 590 sheet: 0.34 (0.33), residues: 238 loop : -0.76 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 60 HIS 0.004 0.001 HIS N 110 PHE 0.012 0.001 PHE C 25 TYR 0.029 0.002 TYR D 40 ARG 0.010 0.000 ARG N 37 *********************** 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 220 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8397 (mt) REVERT: A 94 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6821 (mm-30) REVERT: B 95 ARG cc_start: 0.7795 (mmt-90) cc_final: 0.7496 (mpt180) REVERT: E 50 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7146 (mt-10) REVERT: E 112 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8600 (mp) outliers start: 33 outliers final: 27 residues processed: 207 average time/residue: 0.3203 time to fit residues: 97.5570 Evaluate side-chains 209 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 30 MET Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 245 CYS Chi-restraints excluded: chain N residue 257 ASP 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: 0.0570 chunk 147 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3384 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= 0.203 Angle : 0.584 13.662 28023 Z= 0.340 Chirality : 0.035 0.149 3154 Planarity : 0.004 0.041 2171 Dihedral : 29.836 176.732 5718 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.72 % Allowed : 16.95 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1272 helix: 1.63 (0.21), residues: 590 sheet: 0.41 (0.33), residues: 238 loop : -0.74 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 60 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.001 PHE E 67 TYR 0.027 0.001 TYR D 40 ARG 0.010 0.000 ARG N 37 ********************** 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 211 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 95 ARG cc_start: 0.7757 (mmt-90) cc_final: 0.7474 (mpt180) REVERT: E 50 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7149 (mt-10) REVERT: E 112 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8465 (mp) REVERT: M 123 LEU cc_start: 0.8327 (tt) cc_final: 0.7946 (tp) outliers start: 30 outliers final: 27 residues processed: 200 average time/residue: 0.3237 time to fit residues: 95.3073 Evaluate side-chains 201 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 30 MET Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 245 CYS Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.165512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.119149 restraints weight = 30000.205| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.85 r_work: 0.3423 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3447 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= 0.280 Angle : 0.621 13.303 28023 Z= 0.359 Chirality : 0.037 0.158 3154 Planarity : 0.004 0.041 2171 Dihedral : 30.029 178.050 5718 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.90 % Allowed : 16.95 % Favored : 80.15 % 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: 0.53 (0.23), residues: 1272 helix: 1.29 (0.20), residues: 590 sheet: 0.33 (0.33), residues: 238 loop : -0.85 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 60 HIS 0.005 0.001 HIS N 110 PHE 0.013 0.001 PHE C 25 TYR 0.027 0.002 TYR D 40 ARG 0.010 0.001 ARG N 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3838.63 seconds wall clock time: 70 minutes 27.61 seconds (4227.61 seconds total)