Starting phenix.real_space_refine on Fri Feb 16 16:53:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/02_2024/7cr3_30446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/02_2024/7cr3_30446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/02_2024/7cr3_30446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/02_2024/7cr3_30446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/02_2024/7cr3_30446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/02_2024/7cr3_30446.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 10240 2.51 5 N 2716 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 155": "NH1" <-> "NH2" Residue "G GLU 254": "OE1" <-> "OE2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15924 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2855 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 6, 'TRANS': 342} Chain breaks: 2 Chain: "F" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2855 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 6, 'TRANS': 342} Chain breaks: 2 Chain: "C" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2855 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 6, 'TRANS': 342} Chain breaks: 2 Chain: "E" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2855 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 6, 'TRANS': 342} Chain breaks: 2 Chain: "H" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Time building chain proxies: 9.24, per 1000 atoms: 0.58 Number of scatterers: 15924 At special positions: 0 Unit cell: (124.722, 124.722, 119.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 2880 8.00 N 2716 7.00 C 10240 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: 7.56 Conformation dependent library (CDL) restraints added in 2.8 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 80.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 115 removed outlier: 3.949A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.693A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.892A pdb=" N GLY A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.718A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.555A pdb=" N THR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 removed outlier: 4.784A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 329 removed outlier: 3.914A pdb=" N GLY A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.546A pdb=" N THR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 559 Processing helix chain 'A' and resid 563 through 594 removed outlier: 3.721A pdb=" N VAL A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.640A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.690A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 138 through 146 removed outlier: 3.672A pdb=" N PHE F 142 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 115 removed outlier: 3.949A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.693A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.892A pdb=" N GLY B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.718A pdb=" N MET B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.555A pdb=" N THR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 305 removed outlier: 4.784A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 329 removed outlier: 3.914A pdb=" N GLY B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.546A pdb=" N THR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 559 Processing helix chain 'B' and resid 563 through 594 removed outlier: 3.721A pdb=" N VAL B 567 " --> pdb=" O ASP B 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 66 through 75 removed outlier: 3.639A pdb=" N ARG C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.689A pdb=" N PHE C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 138 through 146 removed outlier: 3.672A pdb=" N PHE C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 115 removed outlier: 3.949A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 4.693A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.892A pdb=" N GLY D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.718A pdb=" N MET D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 254 Processing helix chain 'D' and resid 263 through 276 removed outlier: 3.555A pdb=" N THR D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 305 removed outlier: 4.784A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 329 removed outlier: 3.914A pdb=" N GLY D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 350 Processing helix chain 'D' and resid 357 through 366 removed outlier: 3.546A pdb=" N THR D 366 " --> pdb=" O TYR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 559 Processing helix chain 'D' and resid 563 through 594 removed outlier: 3.721A pdb=" N VAL D 567 " --> pdb=" O ASP D 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 66 through 75 removed outlier: 3.640A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.690A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 138 through 146 removed outlier: 3.672A pdb=" N PHE E 142 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 115 removed outlier: 3.949A pdb=" N TYR G 95 " --> pdb=" O TRP G 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 4.693A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 removed outlier: 3.892A pdb=" N GLY G 159 " --> pdb=" O ARG G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 184 Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.718A pdb=" N MET G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 254 Processing helix chain 'G' and resid 263 through 276 removed outlier: 3.555A pdb=" N THR G 276 " --> pdb=" O LEU G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 305 removed outlier: 4.784A pdb=" N LEU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 329 removed outlier: 3.914A pdb=" N GLY G 310 " --> pdb=" O ALA G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 350 Processing helix chain 'G' and resid 357 through 366 removed outlier: 3.546A pdb=" N THR G 366 " --> pdb=" O TYR G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 559 Processing helix chain 'G' and resid 563 through 594 removed outlier: 3.721A pdb=" N VAL G 567 " --> pdb=" O ASP G 563 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.640A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 80 Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.690A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 146 removed outlier: 3.672A pdb=" N PHE H 142 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AA3, first strand: chain 'E' and resid 27 through 29 Processing sheet with id=AA4, first strand: chain 'H' and resid 27 through 29 1157 hydrogen bonds defined for protein. 3447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 7.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5144 1.34 - 1.46: 3851 1.46 - 1.58: 7113 1.58 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 16256 Sorted by residual: bond pdb=" CB LYS C 31 " pdb=" CG LYS C 31 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.30e-01 bond pdb=" CB LYS E 31 " pdb=" CG LYS E 31 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CB LYS F 31 " pdb=" CG LYS F 31 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CB LYS H 31 " pdb=" CG LYS H 31 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" C LEU B 307 " pdb=" N PRO B 308 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.28e-02 6.10e+03 5.10e-01 ... (remaining 16251 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.10: 252 107.10 - 113.82: 8917 113.82 - 120.54: 7419 120.54 - 127.26: 5199 127.26 - 133.97: 137 Bond angle restraints: 21924 Sorted by residual: angle pdb=" N GLY E 114 " pdb=" CA GLY E 114 " pdb=" C GLY E 114 " ideal model delta sigma weight residual 110.77 115.23 -4.46 1.93e+00 2.68e-01 5.34e+00 angle pdb=" N GLY F 114 " pdb=" CA GLY F 114 " pdb=" C GLY F 114 " ideal model delta sigma weight residual 110.77 115.23 -4.46 1.93e+00 2.68e-01 5.34e+00 angle pdb=" N GLY H 114 " pdb=" CA GLY H 114 " pdb=" C GLY H 114 " ideal model delta sigma weight residual 110.77 115.23 -4.46 1.93e+00 2.68e-01 5.34e+00 angle pdb=" N GLY C 114 " pdb=" CA GLY C 114 " pdb=" C GLY C 114 " ideal model delta sigma weight residual 110.77 115.20 -4.43 1.93e+00 2.68e-01 5.26e+00 angle pdb=" NE ARG A 581 " pdb=" CZ ARG A 581 " pdb=" NH1 ARG A 581 " ideal model delta sigma weight residual 121.50 119.23 2.27 1.00e+00 1.00e+00 5.14e+00 ... (remaining 21919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8432 17.07 - 34.14: 936 34.14 - 51.21: 196 51.21 - 68.28: 24 68.28 - 85.35: 8 Dihedral angle restraints: 9596 sinusoidal: 3896 harmonic: 5700 Sorted by residual: dihedral pdb=" CA PHE E 93 " pdb=" C PHE E 93 " pdb=" N ASP E 94 " pdb=" CA ASP E 94 " ideal model delta harmonic sigma weight residual 180.00 164.33 15.67 0 5.00e+00 4.00e-02 9.82e+00 dihedral pdb=" CA PHE H 93 " pdb=" C PHE H 93 " pdb=" N ASP H 94 " pdb=" CA ASP H 94 " ideal model delta harmonic sigma weight residual 180.00 164.33 15.67 0 5.00e+00 4.00e-02 9.82e+00 dihedral pdb=" CA PHE F 93 " pdb=" C PHE F 93 " pdb=" N ASP F 94 " pdb=" CA ASP F 94 " ideal model delta harmonic sigma weight residual 180.00 164.33 15.67 0 5.00e+00 4.00e-02 9.82e+00 ... (remaining 9593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1348 0.027 - 0.054: 736 0.054 - 0.081: 256 0.081 - 0.108: 48 0.108 - 0.135: 16 Chirality restraints: 2404 Sorted by residual: chirality pdb=" CA ILE C 101 " pdb=" N ILE C 101 " pdb=" C ILE C 101 " pdb=" CB ILE C 101 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE H 101 " pdb=" N ILE H 101 " pdb=" C ILE H 101 " pdb=" CB ILE H 101 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE E 101 " pdb=" N ILE E 101 " pdb=" C ILE E 101 " pdb=" CB ILE E 101 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 2401 not shown) Planarity restraints: 2768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 66 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO E 67 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 66 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO F 67 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 67 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 67 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO H 67 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.021 5.00e-02 4.00e+02 ... (remaining 2765 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3163 2.77 - 3.30: 16950 3.30 - 3.83: 27407 3.83 - 4.37: 32026 4.37 - 4.90: 51243 Nonbonded interactions: 130789 Sorted by model distance: nonbonded pdb=" ND2 ASN B 79 " pdb=" OH TYR C 100 " model vdw 2.232 2.520 nonbonded pdb=" NE2 GLN B 341 " pdb=" O LEU C 113 " model vdw 2.232 2.520 nonbonded pdb=" ND2 ASN A 79 " pdb=" OH TYR F 100 " model vdw 2.238 2.520 nonbonded pdb=" ND2 ASN G 79 " pdb=" OH TYR H 100 " model vdw 2.238 2.520 nonbonded pdb=" ND2 ASN D 79 " pdb=" OH TYR E 100 " model vdw 2.238 2.520 ... (remaining 130784 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 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.970 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 45.600 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.002 0.022 16256 Z= 0.150 Angle : 0.546 7.079 21924 Z= 0.336 Chirality : 0.036 0.135 2404 Planarity : 0.003 0.037 2768 Dihedral : 14.563 85.347 5932 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: -3.24 (0.15), residues: 1936 helix: -1.78 (0.10), residues: 1492 sheet: None (None), residues: 0 loop : -2.80 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 360 HIS 0.002 0.001 HIS A 328 PHE 0.010 0.001 PHE A 240 TYR 0.009 0.001 TYR B 74 ARG 0.002 0.000 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TRP cc_start: 0.6879 (m100) cc_final: 0.6621 (t60) REVERT: A 237 TYR cc_start: 0.8526 (t80) cc_final: 0.7756 (t80) REVERT: A 555 PHE cc_start: 0.6555 (t80) cc_final: 0.6221 (t80) REVERT: F 28 ILE cc_start: 0.5918 (mm) cc_final: 0.5589 (mm) REVERT: F 86 ILE cc_start: 0.5103 (tt) cc_final: 0.4820 (tt) REVERT: B 157 TRP cc_start: 0.6872 (m100) cc_final: 0.6629 (t60) REVERT: B 237 TYR cc_start: 0.8526 (t80) cc_final: 0.7771 (t80) REVERT: B 555 PHE cc_start: 0.6563 (t80) cc_final: 0.6214 (t80) REVERT: C 28 ILE cc_start: 0.5904 (mm) cc_final: 0.5548 (mm) REVERT: C 86 ILE cc_start: 0.5150 (tt) cc_final: 0.4910 (tt) REVERT: D 157 TRP cc_start: 0.6874 (m100) cc_final: 0.6621 (t60) REVERT: D 237 TYR cc_start: 0.8536 (t80) cc_final: 0.7783 (t80) REVERT: D 555 PHE cc_start: 0.6567 (t80) cc_final: 0.6208 (t80) REVERT: E 28 ILE cc_start: 0.5954 (mm) cc_final: 0.5639 (mm) REVERT: E 86 ILE cc_start: 0.5113 (tt) cc_final: 0.4836 (tt) REVERT: G 157 TRP cc_start: 0.6864 (m100) cc_final: 0.6612 (t60) REVERT: G 237 TYR cc_start: 0.8540 (t80) cc_final: 0.7773 (t80) REVERT: G 555 PHE cc_start: 0.6556 (t80) cc_final: 0.6207 (t80) REVERT: H 28 ILE cc_start: 0.5930 (mm) cc_final: 0.5608 (mm) REVERT: H 86 ILE cc_start: 0.5099 (tt) cc_final: 0.4827 (tt) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.3546 time to fit residues: 201.4673 Evaluate side-chains 290 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 0.0870 chunk 80 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 HIS A 350 ASN A 575 HIS ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 350 ASN B 575 HIS C 144 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS D 350 ASN D 575 HIS ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 HIS G 350 ASN G 575 HIS ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16256 Z= 0.236 Angle : 0.643 8.189 21924 Z= 0.329 Chirality : 0.040 0.223 2404 Planarity : 0.004 0.035 2768 Dihedral : 4.316 17.717 2180 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.61 % Allowed : 14.94 % Favored : 83.45 % 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: -1.19 (0.17), residues: 1936 helix: -0.24 (0.12), residues: 1528 sheet: None (None), residues: 0 loop : -2.53 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 288 HIS 0.002 0.001 HIS A 324 PHE 0.020 0.002 PHE H 90 TYR 0.015 0.001 TYR A 74 ARG 0.008 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 349 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: A 157 TRP cc_start: 0.6842 (m100) cc_final: 0.6546 (t60) REVERT: A 204 GLN cc_start: 0.7218 (mt0) cc_final: 0.7008 (mt0) REVERT: A 237 TYR cc_start: 0.8524 (t80) cc_final: 0.7752 (t80) REVERT: A 546 MET cc_start: 0.6007 (tpp) cc_final: 0.5667 (tpp) REVERT: B 142 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: B 157 TRP cc_start: 0.6837 (m100) cc_final: 0.6555 (t60) REVERT: B 204 GLN cc_start: 0.7234 (mt0) cc_final: 0.7028 (mt0) REVERT: B 237 TYR cc_start: 0.8526 (t80) cc_final: 0.7762 (t80) REVERT: B 546 MET cc_start: 0.6043 (tpp) cc_final: 0.5684 (tpp) REVERT: D 142 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: D 157 TRP cc_start: 0.6835 (m100) cc_final: 0.6545 (t60) REVERT: D 204 GLN cc_start: 0.7249 (mt0) cc_final: 0.7045 (mt0) REVERT: D 237 TYR cc_start: 0.8533 (t80) cc_final: 0.7772 (t80) REVERT: D 546 MET cc_start: 0.6013 (tpp) cc_final: 0.5679 (tpp) REVERT: G 142 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: G 157 TRP cc_start: 0.6829 (m100) cc_final: 0.6538 (t60) REVERT: G 204 GLN cc_start: 0.7241 (mt0) cc_final: 0.7031 (mt0) REVERT: G 237 TYR cc_start: 0.8538 (t80) cc_final: 0.7768 (t80) REVERT: G 546 MET cc_start: 0.5991 (tpp) cc_final: 0.5661 (tpp) outliers start: 27 outliers final: 16 residues processed: 361 average time/residue: 0.3529 time to fit residues: 179.5800 Evaluate side-chains 314 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 294 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain G residue 324 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 0.0870 chunk 59 optimal weight: 0.0770 chunk 140 optimal weight: 1.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16256 Z= 0.178 Angle : 0.637 13.300 21924 Z= 0.318 Chirality : 0.039 0.142 2404 Planarity : 0.003 0.028 2768 Dihedral : 4.059 16.747 2180 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.37 % Allowed : 19.52 % Favored : 79.11 % 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: -0.05 (0.18), residues: 1936 helix: 0.58 (0.12), residues: 1548 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 344 HIS 0.002 0.001 HIS A 328 PHE 0.019 0.001 PHE G 555 TYR 0.017 0.001 TYR C 100 ARG 0.005 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 355 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7758 (pp30) cc_final: 0.7527 (tp40) REVERT: A 142 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: A 157 TRP cc_start: 0.6850 (m100) cc_final: 0.6567 (t60) REVERT: A 237 TYR cc_start: 0.8496 (t80) cc_final: 0.7808 (t80) REVERT: A 341 GLN cc_start: 0.6739 (mt0) cc_final: 0.6413 (mt0) REVERT: A 546 MET cc_start: 0.5972 (tpp) cc_final: 0.5474 (tpp) REVERT: F 38 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7814 (ptt90) REVERT: B 78 GLN cc_start: 0.7773 (pp30) cc_final: 0.7465 (tp40) REVERT: B 142 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: B 157 TRP cc_start: 0.6844 (m100) cc_final: 0.6575 (t60) REVERT: B 237 TYR cc_start: 0.8495 (t80) cc_final: 0.7817 (t80) REVERT: B 546 MET cc_start: 0.6062 (tpp) cc_final: 0.5534 (tpp) REVERT: D 78 GLN cc_start: 0.7760 (pp30) cc_final: 0.7527 (tp40) REVERT: D 142 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: D 157 TRP cc_start: 0.6845 (m100) cc_final: 0.6563 (t60) REVERT: D 237 TYR cc_start: 0.8501 (t80) cc_final: 0.7823 (t80) REVERT: D 341 GLN cc_start: 0.6762 (mt0) cc_final: 0.6245 (mt0) REVERT: D 546 MET cc_start: 0.5981 (tpp) cc_final: 0.5493 (tpp) REVERT: E 38 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7813 (ptt90) REVERT: G 78 GLN cc_start: 0.7769 (pp30) cc_final: 0.7536 (tp40) REVERT: G 142 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: G 157 TRP cc_start: 0.6833 (m100) cc_final: 0.6557 (t60) REVERT: G 237 TYR cc_start: 0.8508 (t80) cc_final: 0.7815 (t80) REVERT: G 341 GLN cc_start: 0.6750 (mt0) cc_final: 0.6550 (mt0) REVERT: G 546 MET cc_start: 0.5958 (tpp) cc_final: 0.5475 (tpp) REVERT: H 38 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7804 (ptt90) REVERT: H 40 LEU cc_start: 0.7545 (pp) cc_final: 0.7345 (pp) outliers start: 23 outliers final: 16 residues processed: 367 average time/residue: 0.3194 time to fit residues: 164.2188 Evaluate side-chains 323 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 303 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 324 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16256 Z= 0.276 Angle : 0.669 8.800 21924 Z= 0.345 Chirality : 0.042 0.210 2404 Planarity : 0.003 0.026 2768 Dihedral : 4.248 18.606 2180 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.51 % Allowed : 19.05 % Favored : 77.44 % 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: 0.09 (0.18), residues: 1936 helix: 0.62 (0.12), residues: 1560 sheet: None (None), residues: 0 loop : -2.07 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 157 HIS 0.003 0.001 HIS D 96 PHE 0.021 0.002 PHE B 555 TYR 0.018 0.002 TYR C 100 ARG 0.022 0.001 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 303 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6729 (tmtt) cc_final: 0.5860 (mtpp) REVERT: A 78 GLN cc_start: 0.7849 (pp30) cc_final: 0.7513 (tt0) REVERT: A 142 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: A 157 TRP cc_start: 0.6861 (m100) cc_final: 0.6556 (t60) REVERT: A 204 GLN cc_start: 0.7406 (mt0) cc_final: 0.6970 (mt0) REVERT: A 237 TYR cc_start: 0.8493 (t80) cc_final: 0.7812 (t80) REVERT: A 321 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: A 544 CYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5992 (m) REVERT: A 546 MET cc_start: 0.5973 (tpp) cc_final: 0.5421 (tpp) REVERT: B 76 LYS cc_start: 0.6660 (tmtt) cc_final: 0.5858 (mtpp) REVERT: B 78 GLN cc_start: 0.7861 (pp30) cc_final: 0.7453 (tt0) REVERT: B 142 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: B 157 TRP cc_start: 0.6863 (m100) cc_final: 0.6559 (t60) REVERT: B 204 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6957 (mt0) REVERT: B 237 TYR cc_start: 0.8477 (t80) cc_final: 0.7811 (t80) REVERT: B 321 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: C 40 LEU cc_start: 0.7609 (pp) cc_final: 0.7377 (pp) REVERT: C 106 LEU cc_start: 0.6795 (mt) cc_final: 0.6181 (mt) REVERT: D 76 LYS cc_start: 0.6718 (tmtt) cc_final: 0.5908 (mtpp) REVERT: D 78 GLN cc_start: 0.7867 (pp30) cc_final: 0.7505 (tt0) REVERT: D 142 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: D 157 TRP cc_start: 0.6862 (m100) cc_final: 0.6549 (t60) REVERT: D 204 GLN cc_start: 0.7408 (mt0) cc_final: 0.6975 (mt0) REVERT: D 237 TYR cc_start: 0.8504 (t80) cc_final: 0.7845 (t80) REVERT: D 321 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: D 544 CYS cc_start: 0.6633 (OUTLIER) cc_final: 0.6026 (m) REVERT: D 546 MET cc_start: 0.5924 (tpp) cc_final: 0.5329 (tpp) REVERT: G 76 LYS cc_start: 0.6543 (tmtt) cc_final: 0.5870 (mtpp) REVERT: G 78 GLN cc_start: 0.7851 (pp30) cc_final: 0.7573 (tt0) REVERT: G 142 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: G 157 TRP cc_start: 0.6837 (m100) cc_final: 0.6544 (t60) REVERT: G 204 GLN cc_start: 0.7438 (mt0) cc_final: 0.7001 (mt0) REVERT: G 237 TYR cc_start: 0.8487 (t80) cc_final: 0.7818 (t80) REVERT: G 321 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: G 544 CYS cc_start: 0.6554 (OUTLIER) cc_final: 0.5967 (m) REVERT: G 546 MET cc_start: 0.5910 (tpp) cc_final: 0.5365 (tpp) outliers start: 59 outliers final: 27 residues processed: 344 average time/residue: 0.3108 time to fit residues: 151.0345 Evaluate side-chains 308 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 269 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 544 CYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 321 GLN Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain G residue 544 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 166 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 83 ASN A 341 GLN A 361 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN B 361 GLN D 79 ASN D 83 ASN D 341 GLN D 361 GLN ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 341 GLN G 361 GLN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16256 Z= 0.193 Angle : 0.632 10.485 21924 Z= 0.323 Chirality : 0.040 0.179 2404 Planarity : 0.003 0.025 2768 Dihedral : 4.070 16.671 2180 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.80 % Allowed : 20.18 % Favored : 77.02 % 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 (0.19), residues: 1936 helix: 0.90 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -1.78 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 157 HIS 0.002 0.001 HIS B 575 PHE 0.010 0.001 PHE B 240 TYR 0.015 0.001 TYR C 100 ARG 0.004 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 307 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6676 (tmtt) cc_final: 0.5863 (mtpp) REVERT: A 78 GLN cc_start: 0.7746 (pp30) cc_final: 0.7522 (tt0) REVERT: A 142 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: A 157 TRP cc_start: 0.6854 (m100) cc_final: 0.6563 (t60) REVERT: A 237 TYR cc_start: 0.8486 (t80) cc_final: 0.7877 (t80) REVERT: A 544 CYS cc_start: 0.6380 (OUTLIER) cc_final: 0.5798 (m) REVERT: A 546 MET cc_start: 0.5869 (tpp) cc_final: 0.5304 (tpp) REVERT: B 76 LYS cc_start: 0.6623 (tmtt) cc_final: 0.5846 (mtpp) REVERT: B 78 GLN cc_start: 0.7801 (pp30) cc_final: 0.7485 (tt0) REVERT: B 142 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: B 157 TRP cc_start: 0.6884 (m100) cc_final: 0.6603 (t60) REVERT: B 237 TYR cc_start: 0.8486 (t80) cc_final: 0.7881 (t80) REVERT: B 546 MET cc_start: 0.5844 (tpp) cc_final: 0.5285 (tpp) REVERT: D 76 LYS cc_start: 0.6507 (tmtt) cc_final: 0.5874 (mtpp) REVERT: D 78 GLN cc_start: 0.7774 (pp30) cc_final: 0.7567 (tt0) REVERT: D 142 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: D 157 TRP cc_start: 0.6886 (m100) cc_final: 0.6594 (t60) REVERT: D 237 TYR cc_start: 0.8488 (t80) cc_final: 0.7884 (t80) REVERT: D 544 CYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5770 (m) REVERT: D 546 MET cc_start: 0.5925 (tpp) cc_final: 0.5359 (tpp) REVERT: E 73 MET cc_start: -0.0039 (mmt) cc_final: -0.0528 (mmt) REVERT: G 76 LYS cc_start: 0.6479 (tmtt) cc_final: 0.5873 (mtpp) REVERT: G 78 GLN cc_start: 0.7792 (pp30) cc_final: 0.7583 (tt0) REVERT: G 142 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: G 157 TRP cc_start: 0.6878 (m100) cc_final: 0.6577 (t60) REVERT: G 237 TYR cc_start: 0.8511 (t80) cc_final: 0.7913 (t80) REVERT: G 544 CYS cc_start: 0.6245 (OUTLIER) cc_final: 0.5674 (m) REVERT: G 546 MET cc_start: 0.5918 (tpp) cc_final: 0.5295 (tpp) outliers start: 47 outliers final: 22 residues processed: 342 average time/residue: 0.2983 time to fit residues: 145.7933 Evaluate side-chains 315 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 286 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 544 CYS Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 86 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN G 83 ASN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16256 Z= 0.194 Angle : 0.660 13.300 21924 Z= 0.333 Chirality : 0.040 0.165 2404 Planarity : 0.003 0.042 2768 Dihedral : 4.021 16.972 2180 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.98 % Allowed : 20.77 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 1936 helix: 1.06 (0.13), residues: 1556 sheet: None (None), residues: 0 loop : -1.71 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 344 HIS 0.002 0.001 HIS D 575 PHE 0.015 0.001 PHE D 240 TYR 0.015 0.001 TYR H 139 ARG 0.008 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 301 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6715 (tmtt) cc_final: 0.5878 (mtpp) REVERT: A 142 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: A 237 TYR cc_start: 0.8476 (t80) cc_final: 0.7880 (t80) REVERT: A 249 LEU cc_start: 0.9345 (mt) cc_final: 0.9055 (mp) REVERT: A 544 CYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5686 (m) REVERT: A 546 MET cc_start: 0.5940 (tpp) cc_final: 0.5328 (tpp) REVERT: F 72 MET cc_start: 0.0218 (tmm) cc_final: -0.0025 (tmm) REVERT: B 76 LYS cc_start: 0.6482 (tmtt) cc_final: 0.5851 (mtpp) REVERT: B 78 GLN cc_start: 0.7771 (pp30) cc_final: 0.7494 (tt0) REVERT: B 142 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: B 204 GLN cc_start: 0.7291 (mt0) cc_final: 0.6864 (mt0) REVERT: B 237 TYR cc_start: 0.8511 (t80) cc_final: 0.7920 (t80) REVERT: B 249 LEU cc_start: 0.9343 (mt) cc_final: 0.9053 (mp) REVERT: D 76 LYS cc_start: 0.6708 (tmtt) cc_final: 0.5924 (mtpp) REVERT: D 142 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: D 237 TYR cc_start: 0.8510 (t80) cc_final: 0.7976 (t80) REVERT: D 249 LEU cc_start: 0.9350 (mt) cc_final: 0.9060 (mp) REVERT: D 544 CYS cc_start: 0.6363 (OUTLIER) cc_final: 0.5679 (m) REVERT: D 546 MET cc_start: 0.5951 (tpp) cc_final: 0.5350 (tpp) REVERT: G 76 LYS cc_start: 0.6479 (tmtt) cc_final: 0.5869 (mtpp) REVERT: G 78 GLN cc_start: 0.7794 (pp30) cc_final: 0.7565 (tt0) REVERT: G 142 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: G 237 TYR cc_start: 0.8491 (t80) cc_final: 0.7892 (t80) REVERT: G 249 LEU cc_start: 0.9349 (mt) cc_final: 0.9055 (mp) REVERT: G 546 MET cc_start: 0.5999 (tpp) cc_final: 0.5299 (tpp) REVERT: H 72 MET cc_start: 0.0172 (tmm) cc_final: -0.0068 (tmm) outliers start: 50 outliers final: 38 residues processed: 336 average time/residue: 0.3002 time to fit residues: 145.1729 Evaluate side-chains 314 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 544 CYS Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 83 ASN A 204 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 83 ASN D 204 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16256 Z= 0.228 Angle : 0.712 13.893 21924 Z= 0.356 Chirality : 0.041 0.172 2404 Planarity : 0.004 0.068 2768 Dihedral : 4.058 16.249 2180 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.87 % Allowed : 21.13 % Favored : 75.00 % 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: 0.77 (0.19), residues: 1936 helix: 1.03 (0.13), residues: 1572 sheet: None (None), residues: 0 loop : -1.54 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 146 HIS 0.003 0.001 HIS B 575 PHE 0.015 0.001 PHE D 240 TYR 0.012 0.001 TYR C 100 ARG 0.007 0.001 ARG D 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 280 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6648 (tmtt) cc_final: 0.5864 (mtpp) REVERT: A 142 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: A 237 TYR cc_start: 0.8498 (t80) cc_final: 0.7856 (t80) REVERT: A 321 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: A 544 CYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5903 (m) REVERT: A 546 MET cc_start: 0.5951 (tpp) cc_final: 0.5344 (tpp) REVERT: B 76 LYS cc_start: 0.6569 (tmtt) cc_final: 0.5918 (mtpp) REVERT: B 78 GLN cc_start: 0.7730 (pp30) cc_final: 0.7442 (tt0) REVERT: B 142 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: B 237 TYR cc_start: 0.8497 (t80) cc_final: 0.7850 (t80) REVERT: B 321 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: B 546 MET cc_start: 0.5878 (tpp) cc_final: 0.5240 (tpp) REVERT: C 72 MET cc_start: 0.0694 (tmm) cc_final: 0.0478 (tmm) REVERT: D 76 LYS cc_start: 0.6437 (tmtt) cc_final: 0.5876 (mtpp) REVERT: D 142 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: D 237 TYR cc_start: 0.8506 (t80) cc_final: 0.7924 (t80) REVERT: D 321 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: D 332 ARG cc_start: 0.7445 (ttp-110) cc_final: 0.6873 (ttm-80) REVERT: D 544 CYS cc_start: 0.6479 (OUTLIER) cc_final: 0.5818 (m) REVERT: D 546 MET cc_start: 0.5943 (tpp) cc_final: 0.5313 (tpp) REVERT: G 76 LYS cc_start: 0.6769 (tmtt) cc_final: 0.5966 (mtpp) REVERT: G 142 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: G 237 TYR cc_start: 0.8522 (t80) cc_final: 0.7941 (t80) REVERT: G 321 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: G 546 MET cc_start: 0.5890 (tpp) cc_final: 0.5290 (tpp) REVERT: H 146 MET cc_start: 0.5529 (mtt) cc_final: 0.5043 (mtt) outliers start: 65 outliers final: 39 residues processed: 326 average time/residue: 0.2711 time to fit residues: 131.0699 Evaluate side-chains 315 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 266 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 544 CYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 321 GLN Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 145 optimal weight: 0.0670 chunk 168 optimal weight: 4.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 204 GLN G 79 ASN G 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16256 Z= 0.200 Angle : 0.732 14.608 21924 Z= 0.359 Chirality : 0.041 0.172 2404 Planarity : 0.003 0.025 2768 Dihedral : 4.015 17.317 2180 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.92 % Allowed : 22.80 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1936 helix: 1.11 (0.13), residues: 1556 sheet: None (None), residues: 0 loop : -1.45 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 344 HIS 0.002 0.001 HIS A 260 PHE 0.030 0.001 PHE H 20 TYR 0.020 0.001 TYR F 100 ARG 0.005 0.000 ARG E 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 278 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6656 (tmtt) cc_final: 0.5838 (mtpp) REVERT: A 142 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: A 237 TYR cc_start: 0.8485 (t80) cc_final: 0.7927 (t80) REVERT: A 321 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: A 546 MET cc_start: 0.5912 (tpp) cc_final: 0.5310 (tpp) REVERT: F 110 MET cc_start: 0.5988 (tpt) cc_final: 0.5778 (tmm) REVERT: B 76 LYS cc_start: 0.6308 (tmtt) cc_final: 0.5738 (mtpp) REVERT: B 142 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: B 204 GLN cc_start: 0.7393 (mt0) cc_final: 0.6982 (mt0) REVERT: B 237 TYR cc_start: 0.8485 (t80) cc_final: 0.7919 (t80) REVERT: B 321 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: B 546 MET cc_start: 0.5808 (tpp) cc_final: 0.5200 (tpp) REVERT: C 72 MET cc_start: 0.1082 (tmm) cc_final: 0.0683 (tmm) REVERT: D 76 LYS cc_start: 0.6447 (tmtt) cc_final: 0.5865 (mtpp) REVERT: D 142 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: D 237 TYR cc_start: 0.8489 (t80) cc_final: 0.7923 (t80) REVERT: D 321 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: D 546 MET cc_start: 0.5949 (tpp) cc_final: 0.5310 (tpp) REVERT: G 76 LYS cc_start: 0.6388 (tmtt) cc_final: 0.5863 (mtpp) REVERT: G 142 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: G 237 TYR cc_start: 0.8493 (t80) cc_final: 0.7938 (t80) REVERT: G 321 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: G 332 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.7353 (ttm-80) REVERT: G 546 MET cc_start: 0.5877 (tpp) cc_final: 0.5303 (tpp) outliers start: 49 outliers final: 36 residues processed: 313 average time/residue: 0.2837 time to fit residues: 130.0429 Evaluate side-chains 307 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 263 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 321 GLN Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 40.0000 chunk 113 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 78 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN D 357 HIS ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16256 Z= 0.274 Angle : 0.791 15.583 21924 Z= 0.386 Chirality : 0.042 0.173 2404 Planarity : 0.004 0.047 2768 Dihedral : 4.149 17.273 2180 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.33 % Allowed : 23.04 % Favored : 73.63 % 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: 0.63 (0.19), residues: 1936 helix: 0.89 (0.13), residues: 1556 sheet: None (None), residues: 0 loop : -1.28 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 344 HIS 0.003 0.001 HIS D 575 PHE 0.022 0.002 PHE H 20 TYR 0.018 0.001 TYR E 100 ARG 0.009 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 261 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6731 (tmtt) cc_final: 0.5809 (mtpp) REVERT: A 142 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: A 237 TYR cc_start: 0.8508 (t80) cc_final: 0.7864 (t80) REVERT: A 321 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: A 546 MET cc_start: 0.5909 (tpp) cc_final: 0.5259 (tpp) REVERT: B 76 LYS cc_start: 0.6616 (tmtt) cc_final: 0.5786 (mtpp) REVERT: B 78 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7730 (mm-40) REVERT: B 142 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: B 174 MET cc_start: 0.7316 (ppp) cc_final: 0.7043 (ppp) REVERT: B 237 TYR cc_start: 0.8494 (t80) cc_final: 0.7864 (t80) REVERT: B 321 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: B 546 MET cc_start: 0.5876 (tpp) cc_final: 0.5242 (tpp) REVERT: C 146 MET cc_start: 0.6812 (mmm) cc_final: 0.6151 (mpp) REVERT: D 76 LYS cc_start: 0.6636 (tmtt) cc_final: 0.5834 (mtpp) REVERT: D 142 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: D 237 TYR cc_start: 0.8494 (t80) cc_final: 0.7864 (t80) REVERT: D 321 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: D 546 MET cc_start: 0.5954 (tpp) cc_final: 0.5314 (tpp) REVERT: E 110 MET cc_start: 0.6750 (ppp) cc_final: 0.6257 (ppp) REVERT: G 76 LYS cc_start: 0.6622 (tmtt) cc_final: 0.5778 (mtpp) REVERT: G 142 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: G 237 TYR cc_start: 0.8502 (t80) cc_final: 0.7880 (t80) REVERT: G 321 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: G 546 MET cc_start: 0.5941 (tpp) cc_final: 0.5356 (tpp) outliers start: 56 outliers final: 43 residues processed: 302 average time/residue: 0.2854 time to fit residues: 125.5817 Evaluate side-chains 285 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 233 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 321 GLN Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 78 GLN B 79 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 204 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN G 357 HIS ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16256 Z= 0.292 Angle : 0.788 13.850 21924 Z= 0.390 Chirality : 0.043 0.174 2404 Planarity : 0.003 0.026 2768 Dihedral : 4.222 16.063 2180 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.92 % Allowed : 23.10 % Favored : 73.99 % 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: 0.41 (0.19), residues: 1936 helix: 0.81 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -1.73 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 146 HIS 0.003 0.001 HIS G 260 PHE 0.039 0.002 PHE C 93 TYR 0.019 0.002 TYR H 100 ARG 0.012 0.001 ARG D 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 259 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6742 (tmtt) cc_final: 0.5811 (mtpp) REVERT: A 96 HIS cc_start: 0.6508 (m90) cc_final: 0.6106 (m90) REVERT: A 142 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: A 174 MET cc_start: 0.7285 (ppp) cc_final: 0.6968 (ppp) REVERT: A 237 TYR cc_start: 0.8498 (t80) cc_final: 0.7713 (t80) REVERT: A 321 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: A 546 MET cc_start: 0.5939 (tpp) cc_final: 0.5406 (tpp) REVERT: F 146 MET cc_start: 0.6781 (mmm) cc_final: 0.6114 (mtp) REVERT: B 76 LYS cc_start: 0.6658 (tmtt) cc_final: 0.5806 (mtpp) REVERT: B 78 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7736 (mm-40) REVERT: B 96 HIS cc_start: 0.6517 (m90) cc_final: 0.6119 (m90) REVERT: B 142 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: B 174 MET cc_start: 0.7304 (ppp) cc_final: 0.7025 (ppp) REVERT: B 237 TYR cc_start: 0.8498 (t80) cc_final: 0.7712 (t80) REVERT: B 321 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: B 546 MET cc_start: 0.5986 (tpp) cc_final: 0.5433 (tpp) REVERT: C 146 MET cc_start: 0.6832 (mmm) cc_final: 0.6038 (mtp) REVERT: D 76 LYS cc_start: 0.6734 (tmtt) cc_final: 0.5873 (mtpp) REVERT: D 96 HIS cc_start: 0.6496 (m90) cc_final: 0.6103 (m90) REVERT: D 142 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: D 174 MET cc_start: 0.7240 (ppp) cc_final: 0.6932 (ppp) REVERT: D 237 TYR cc_start: 0.8501 (t80) cc_final: 0.7714 (t80) REVERT: D 321 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: G 76 LYS cc_start: 0.6696 (tmtt) cc_final: 0.5818 (mtpp) REVERT: G 96 HIS cc_start: 0.6493 (m90) cc_final: 0.6106 (m90) REVERT: G 142 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: G 174 MET cc_start: 0.7286 (ppp) cc_final: 0.6973 (ppp) REVERT: G 237 TYR cc_start: 0.8514 (t80) cc_final: 0.7733 (t80) REVERT: G 321 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: G 546 MET cc_start: 0.5950 (tpp) cc_final: 0.5345 (tpp) REVERT: H 146 MET cc_start: 0.5319 (mtt) cc_final: 0.4934 (mtt) outliers start: 49 outliers final: 39 residues processed: 293 average time/residue: 0.2684 time to fit residues: 116.4138 Evaluate side-chains 289 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 241 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 108 HIS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 321 GLN Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 108 HIS Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 204 GLN B 78 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.209102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.173251 restraints weight = 28531.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.164087 restraints weight = 34115.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.161872 restraints weight = 30868.414| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16256 Z= 0.266 Angle : 0.781 13.885 21924 Z= 0.387 Chirality : 0.042 0.175 2404 Planarity : 0.003 0.026 2768 Dihedral : 4.177 16.220 2180 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.92 % Allowed : 23.63 % Favored : 73.45 % 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: 0.44 (0.19), residues: 1936 helix: 0.82 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -1.66 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 360 HIS 0.003 0.001 HIS D 260 PHE 0.034 0.002 PHE C 93 TYR 0.017 0.002 TYR F 100 ARG 0.009 0.001 ARG D 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3383.23 seconds wall clock time: 62 minutes 22.56 seconds (3742.56 seconds total)