Starting phenix.real_space_refine on Fri Sep 27 11:09:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/09_2024/7cr3_30446.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/09_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_30446/09_2024/7cr3_30446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/09_2024/7cr3_30446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/09_2024/7cr3_30446.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr3_30446/09_2024/7cr3_30446.cif" } 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. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15924 Number of models: 1 Model: "" Number of chains: 2 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: "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} Restraints were copied for chains: E, F, H, B, D, G Time building chain proxies: 6.77, per 1000 atoms: 0.43 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 - 3.00 Amino acid : True - 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: 3.68 Conformation dependent library (CDL) restraints added in 2.0 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: 1.36 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: 4.58 Time building geometry restraints manager: 4.28 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: 0.00 - 1.42: 21425 1.42 - 2.83: 407 2.83 - 4.25: 59 4.25 - 5.66: 29 5.66 - 7.08: 4 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 3.120 nonbonded pdb=" NE2 GLN B 341 " pdb=" O LEU C 113 " model vdw 2.232 3.120 nonbonded pdb=" ND2 ASN A 79 " pdb=" OH TYR F 100 " model vdw 2.238 3.120 nonbonded pdb=" ND2 ASN G 79 " pdb=" OH TYR H 100 " model vdw 2.238 3.120 nonbonded pdb=" ND2 ASN D 79 " pdb=" OH TYR E 100 " model vdw 2.238 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.810 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- 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 : 1.718 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: 0.3366 time to fit residues: 191.2280 Evaluate side-chains 290 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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: 5.9990 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** 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 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 350 ASN B 575 HIS C 144 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS D 350 ASN D 357 HIS D 575 HIS ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN ** G 78 GLN ** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16256 Z= 0.300 Angle : 0.688 8.477 21924 Z= 0.354 Chirality : 0.042 0.212 2404 Planarity : 0.004 0.042 2768 Dihedral : 4.414 18.940 2180 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.90 % Allowed : 16.90 % Favored : 81.19 % 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: -1.41 (0.17), residues: 1936 helix: -0.37 (0.12), residues: 1532 sheet: None (None), residues: 0 loop : -2.74 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 157 HIS 0.003 0.001 HIS A 260 PHE 0.022 0.002 PHE H 90 TYR 0.017 0.002 TYR A 74 ARG 0.009 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 383 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 351 time to evaluate : 1.640 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: A 76 LYS cc_start: 0.6853 (tmtt) cc_final: 0.5956 (mtpp) REVERT: A 142 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: A 157 TRP cc_start: 0.6835 (m100) cc_final: 0.6483 (t60) REVERT: A 204 GLN cc_start: 0.7319 (mt0) cc_final: 0.6978 (mm-40) REVERT: A 237 TYR cc_start: 0.8541 (t80) cc_final: 0.7706 (t80) REVERT: A 546 MET cc_start: 0.6019 (tpp) cc_final: 0.5643 (tpp) REVERT: A 555 PHE cc_start: 0.6516 (t80) cc_final: 0.6307 (t80) REVERT: B 76 LYS cc_start: 0.6864 (tmtt) cc_final: 0.5968 (mtpp) REVERT: B 142 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: B 157 TRP cc_start: 0.6833 (m100) cc_final: 0.6492 (t60) REVERT: B 204 GLN cc_start: 0.7330 (mt0) cc_final: 0.6993 (mm-40) REVERT: B 237 TYR cc_start: 0.8566 (t80) cc_final: 0.7739 (t80) REVERT: B 546 MET cc_start: 0.6049 (tpp) cc_final: 0.5694 (tpp) REVERT: B 555 PHE cc_start: 0.6515 (t80) cc_final: 0.6309 (t80) REVERT: C 112 ASN cc_start: 0.8107 (p0) cc_final: 0.7809 (p0) REVERT: D 142 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: D 157 TRP cc_start: 0.6830 (m100) cc_final: 0.6484 (t60) REVERT: D 204 GLN cc_start: 0.7325 (mt0) cc_final: 0.6990 (mm-40) REVERT: D 237 TYR cc_start: 0.8567 (t80) cc_final: 0.7748 (t80) REVERT: D 546 MET cc_start: 0.6026 (tpp) cc_final: 0.5660 (tpp) REVERT: D 555 PHE cc_start: 0.6520 (t80) cc_final: 0.6301 (t80) REVERT: G 76 LYS cc_start: 0.6872 (tmtt) cc_final: 0.5987 (mtpp) REVERT: G 142 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: G 157 TRP cc_start: 0.6823 (m100) cc_final: 0.6475 (t60) REVERT: G 204 GLN cc_start: 0.7313 (mt0) cc_final: 0.6976 (mm-40) REVERT: G 237 TYR cc_start: 0.8577 (t80) cc_final: 0.7747 (t80) REVERT: G 546 MET cc_start: 0.6004 (tpp) cc_final: 0.5646 (tpp) REVERT: G 555 PHE cc_start: 0.6535 (t80) cc_final: 0.6323 (t80) outliers start: 32 outliers final: 25 residues processed: 367 average time/residue: 0.3421 time to fit residues: 176.1980 Evaluate side-chains 309 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 280 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 299 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 84 VAL 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 299 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 VAL 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 299 LEU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain G residue 84 VAL 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 299 LEU 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: 10.0000 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 118 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 357 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN B 357 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN 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: 0.7439 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16256 Z= 0.223 Angle : 0.675 12.386 21924 Z= 0.341 Chirality : 0.040 0.146 2404 Planarity : 0.003 0.025 2768 Dihedral : 4.249 18.003 2180 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.73 % Allowed : 20.24 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 1936 helix: 0.30 (0.12), residues: 1552 sheet: None (None), residues: 0 loop : -2.69 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 344 HIS 0.002 0.001 HIS D 96 PHE 0.015 0.002 PHE H 142 TYR 0.015 0.002 TYR D 347 ARG 0.009 0.000 ARG H 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 367 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 338 time to evaluate : 1.632 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: A 76 LYS cc_start: 0.6739 (tmtt) cc_final: 0.5965 (mtpp) REVERT: A 142 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: A 157 TRP cc_start: 0.6864 (m100) cc_final: 0.6643 (t60) REVERT: A 237 TYR cc_start: 0.8508 (t80) cc_final: 0.7772 (t80) REVERT: A 546 MET cc_start: 0.6081 (tpp) cc_final: 0.5570 (tpp) REVERT: B 76 LYS cc_start: 0.6707 (tmtt) cc_final: 0.5919 (mtpp) REVERT: B 142 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: B 157 TRP cc_start: 0.6859 (m100) cc_final: 0.6652 (t60) REVERT: B 237 TYR cc_start: 0.8547 (t80) cc_final: 0.7745 (t80) REVERT: B 546 MET cc_start: 0.6018 (tpp) cc_final: 0.5494 (tpp) REVERT: C 112 ASN cc_start: 0.8005 (p0) cc_final: 0.7802 (p0) REVERT: D 76 LYS cc_start: 0.6741 (tmtt) cc_final: 0.5945 (mtpp) REVERT: D 142 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: D 157 TRP cc_start: 0.6859 (m100) cc_final: 0.6647 (t60) REVERT: D 237 TYR cc_start: 0.8550 (t80) cc_final: 0.7820 (t80) REVERT: D 546 MET cc_start: 0.6087 (tpp) cc_final: 0.5585 (tpp) REVERT: G 76 LYS cc_start: 0.6751 (tmtt) cc_final: 0.5985 (mtpp) REVERT: G 142 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: G 157 TRP cc_start: 0.6845 (m100) cc_final: 0.6636 (t60) REVERT: G 237 TYR cc_start: 0.8532 (t80) cc_final: 0.7794 (t80) REVERT: G 546 MET cc_start: 0.6073 (tpp) cc_final: 0.5573 (tpp) outliers start: 29 outliers final: 16 residues processed: 354 average time/residue: 0.3218 time to fit residues: 158.6021 Evaluate side-chains 309 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 289 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 361 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 204 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN G 361 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: 0.7459 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16256 Z= 0.253 Angle : 0.678 8.895 21924 Z= 0.347 Chirality : 0.041 0.129 2404 Planarity : 0.003 0.027 2768 Dihedral : 4.261 20.490 2180 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.33 % Allowed : 20.12 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 1936 helix: 0.53 (0.12), residues: 1548 sheet: None (None), residues: 0 loop : -2.20 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 344 HIS 0.002 0.001 HIS G 96 PHE 0.015 0.002 PHE G 555 TYR 0.015 0.002 TYR B 74 ARG 0.006 0.000 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 365 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 309 time to evaluate : 1.696 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: 0.6811 (tmtt) cc_final: 0.5988 (mtpp) REVERT: A 83 ASN cc_start: 0.7505 (m-40) cc_final: 0.7287 (m110) REVERT: A 142 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: A 157 TRP cc_start: 0.6833 (m100) cc_final: 0.6528 (t60) REVERT: A 237 TYR cc_start: 0.8548 (t80) cc_final: 0.7821 (t80) REVERT: A 321 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: B 76 LYS cc_start: 0.6742 (tmtt) cc_final: 0.5919 (mtpp) REVERT: B 142 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: B 157 TRP cc_start: 0.6833 (m100) cc_final: 0.6537 (t60) REVERT: B 237 TYR cc_start: 0.8549 (t80) cc_final: 0.7825 (t80) REVERT: B 321 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: B 546 MET cc_start: 0.6028 (tpp) cc_final: 0.5221 (tpp) REVERT: C 112 ASN cc_start: 0.7986 (p0) cc_final: 0.7752 (p0) REVERT: D 76 LYS cc_start: 0.6885 (tmtt) cc_final: 0.6053 (mtpp) REVERT: D 142 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: D 157 TRP cc_start: 0.6825 (m100) cc_final: 0.6529 (t60) REVERT: D 237 TYR cc_start: 0.8552 (t80) cc_final: 0.7831 (t80) REVERT: D 321 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: G 76 LYS cc_start: 0.6739 (tmtt) cc_final: 0.5925 (mtpp) REVERT: G 83 ASN cc_start: 0.7477 (m-40) cc_final: 0.7266 (m110) REVERT: G 142 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: G 157 TRP cc_start: 0.6811 (m100) cc_final: 0.6517 (t60) REVERT: G 237 TYR cc_start: 0.8559 (t80) cc_final: 0.7835 (t80) REVERT: G 321 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7743 (tm-30) outliers start: 56 outliers final: 32 residues processed: 349 average time/residue: 0.2899 time to fit residues: 143.9492 Evaluate side-chains 322 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 282 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 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 35 THR 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 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 35 THR 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 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 G residue 109 LEU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 142 PHE 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 H residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 158 optimal weight: 0.1980 chunk 128 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN B 361 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN ** E 138 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16256 Z= 0.267 Angle : 0.696 10.182 21924 Z= 0.355 Chirality : 0.041 0.136 2404 Planarity : 0.003 0.027 2768 Dihedral : 4.293 19.064 2180 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.05 % Allowed : 20.36 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 1936 helix: 0.58 (0.12), residues: 1548 sheet: None (None), residues: 0 loop : -1.97 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 157 HIS 0.002 0.001 HIS A 96 PHE 0.014 0.002 PHE D 240 TYR 0.015 0.002 TYR D 74 ARG 0.006 0.000 ARG C 107 *********************** 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 381 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 313 time to evaluate : 1.661 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: A 76 LYS cc_start: 0.6778 (tmtt) cc_final: 0.5908 (mtpp) REVERT: A 83 ASN cc_start: 0.7501 (m-40) cc_final: 0.7284 (m110) REVERT: A 142 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: A 237 TYR cc_start: 0.8552 (t80) cc_final: 0.7763 (t80) REVERT: A 321 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: A 546 MET cc_start: 0.6005 (tpp) cc_final: 0.5469 (tpp) REVERT: F 146 MET cc_start: 0.5806 (mtt) cc_final: 0.5606 (mtm) REVERT: B 76 LYS cc_start: 0.6767 (tmtt) cc_final: 0.5997 (mtpp) REVERT: B 142 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: B 237 TYR cc_start: 0.8556 (t80) cc_final: 0.7884 (t80) REVERT: B 321 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: B 546 MET cc_start: 0.5938 (tpp) cc_final: 0.5367 (tpp) REVERT: C 72 MET cc_start: 0.0257 (tmm) cc_final: 0.0057 (tmt) REVERT: C 96 ASP cc_start: 0.5069 (OUTLIER) cc_final: 0.4536 (p0) REVERT: C 112 ASN cc_start: 0.7992 (p0) cc_final: 0.7748 (p0) REVERT: D 76 LYS cc_start: 0.6813 (tmtt) cc_final: 0.5962 (mtpp) REVERT: D 83 ASN cc_start: 0.7407 (m110) cc_final: 0.7184 (m110) REVERT: D 142 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: D 237 TYR cc_start: 0.8558 (t80) cc_final: 0.7893 (t80) REVERT: D 321 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: E 96 ASP cc_start: 0.5248 (OUTLIER) cc_final: 0.4680 (p0) REVERT: E 146 MET cc_start: 0.5896 (mtt) cc_final: 0.5551 (mtt) REVERT: G 76 LYS cc_start: 0.6802 (tmtt) cc_final: 0.5919 (mtpp) REVERT: G 83 ASN cc_start: 0.7503 (m-40) cc_final: 0.7251 (m110) REVERT: G 142 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: G 237 TYR cc_start: 0.8551 (t80) cc_final: 0.7882 (t80) REVERT: G 321 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: H 96 ASP cc_start: 0.5059 (OUTLIER) cc_final: 0.4521 (p0) outliers start: 68 outliers final: 44 residues processed: 358 average time/residue: 0.2971 time to fit residues: 152.6861 Evaluate side-chains 323 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 268 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 234 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 320 VAL 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 35 THR Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain B residue 84 VAL 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 234 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 320 VAL 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 96 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 234 THR Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 320 VAL 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 96 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 287 THR Chi-restraints excluded: chain G residue 320 VAL 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 H residue 35 THR Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7408 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16256 Z= 0.204 Angle : 0.690 11.475 21924 Z= 0.345 Chirality : 0.040 0.141 2404 Planarity : 0.003 0.044 2768 Dihedral : 4.099 19.681 2180 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.57 % Allowed : 21.67 % Favored : 74.76 % 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: 0.48 (0.18), residues: 1936 helix: 0.90 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -1.93 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 288 HIS 0.002 0.001 HIS B 96 PHE 0.019 0.001 PHE B 555 TYR 0.015 0.001 TYR H 100 ARG 0.009 0.000 ARG A 345 *********************** 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 383 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 323 time to evaluate : 1.676 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: 0.6691 (tmtt) cc_final: 0.5867 (mtpp) REVERT: A 142 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: A 237 TYR cc_start: 0.8342 (t80) cc_final: 0.7595 (t80) REVERT: A 321 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: A 339 LEU cc_start: 0.7531 (mm) cc_final: 0.7131 (mt) REVERT: F 83 GLU cc_start: 0.4833 (tp30) cc_final: 0.3485 (tp30) REVERT: F 96 ASP cc_start: 0.5156 (OUTLIER) cc_final: 0.4681 (p0) REVERT: F 113 LEU cc_start: 0.5060 (OUTLIER) cc_final: 0.4302 (tp) REVERT: B 76 LYS cc_start: 0.6660 (tmtt) cc_final: 0.5905 (mtpp) REVERT: B 83 ASN cc_start: 0.7336 (m-40) cc_final: 0.7098 (m110) REVERT: B 142 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: B 237 TYR cc_start: 0.8524 (t80) cc_final: 0.7905 (t80) REVERT: B 321 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: B 342 SER cc_start: 0.5690 (OUTLIER) cc_final: 0.5335 (p) REVERT: B 546 MET cc_start: 0.5830 (tpp) cc_final: 0.5158 (tpp) REVERT: C 72 MET cc_start: -0.0160 (tmm) cc_final: -0.0396 (tmt) REVERT: C 83 GLU cc_start: 0.5083 (tp30) cc_final: 0.3800 (tp30) REVERT: C 96 ASP cc_start: 0.5055 (OUTLIER) cc_final: 0.4554 (p0) REVERT: D 76 LYS cc_start: 0.6805 (tmtt) cc_final: 0.6030 (mtpp) REVERT: D 142 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7455 (m-80) REVERT: D 237 TYR cc_start: 0.8528 (t80) cc_final: 0.7911 (t80) REVERT: D 321 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: D 342 SER cc_start: 0.5699 (OUTLIER) cc_final: 0.5408 (p) REVERT: E 96 ASP cc_start: 0.5080 (OUTLIER) cc_final: 0.4627 (p0) REVERT: G 76 LYS cc_start: 0.6692 (tmtt) cc_final: 0.5897 (mtpp) REVERT: G 142 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: G 237 TYR cc_start: 0.8532 (t80) cc_final: 0.7914 (t80) REVERT: G 321 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: G 342 SER cc_start: 0.5854 (OUTLIER) cc_final: 0.5419 (p) REVERT: H 96 ASP cc_start: 0.5074 (OUTLIER) cc_final: 0.4562 (p0) outliers start: 60 outliers final: 27 residues processed: 363 average time/residue: 0.2987 time to fit residues: 155.5767 Evaluate side-chains 319 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 276 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 129 LEU Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 273 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 F residue 96 ASP Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain F residue 113 LEU 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 273 ILE 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 B residue 342 SER Chi-restraints excluded: chain C residue 96 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 273 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 342 SER Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 273 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 342 SER Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 0.0030 chunk 114 optimal weight: 0.8980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4822 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= 0.201 Angle : 0.733 11.716 21924 Z= 0.365 Chirality : 0.041 0.171 2404 Planarity : 0.003 0.033 2768 Dihedral : 4.126 26.548 2180 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.27 % Allowed : 23.04 % Favored : 73.69 % 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 (0.18), residues: 1936 helix: 1.06 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -1.74 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 288 HIS 0.002 0.001 HIS D 575 PHE 0.017 0.001 PHE B 555 TYR 0.014 0.001 TYR H 100 ARG 0.007 0.001 ARG G 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 369 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 314 time to evaluate : 1.897 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: A 76 LYS cc_start: 0.6518 (tmtt) cc_final: 0.5889 (mtpp) REVERT: A 142 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: A 237 TYR cc_start: 0.8407 (t80) cc_final: 0.7519 (t80) REVERT: A 321 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: F 73 MET cc_start: 0.0170 (mmt) cc_final: -0.0101 (mtt) REVERT: F 83 GLU cc_start: 0.4798 (tp30) cc_final: 0.3480 (tp30) REVERT: F 96 ASP cc_start: 0.5007 (OUTLIER) cc_final: 0.4519 (p0) REVERT: B 76 LYS cc_start: 0.6443 (tmtt) cc_final: 0.5909 (mtpp) REVERT: B 78 GLN cc_start: 0.7411 (pp30) cc_final: 0.7149 (tp40) REVERT: B 142 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: B 237 TYR cc_start: 0.8532 (t80) cc_final: 0.7931 (t80) REVERT: B 321 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: B 546 MET cc_start: 0.5860 (tpp) cc_final: 0.5291 (tpp) REVERT: C 96 ASP cc_start: 0.5294 (OUTLIER) cc_final: 0.4789 (p0) REVERT: D 76 LYS cc_start: 0.6643 (tmtt) cc_final: 0.6023 (mtpp) REVERT: D 142 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: D 237 TYR cc_start: 0.8535 (t80) cc_final: 0.7939 (t80) REVERT: D 321 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: E 83 GLU cc_start: 0.4235 (tp30) cc_final: 0.3543 (tp30) REVERT: E 96 ASP cc_start: 0.5407 (OUTLIER) cc_final: 0.4881 (p0) REVERT: G 76 LYS cc_start: 0.6639 (tmtt) cc_final: 0.5908 (mtpp) REVERT: G 142 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: G 237 TYR cc_start: 0.8541 (t80) cc_final: 0.7938 (t80) REVERT: G 249 LEU cc_start: 0.9366 (mt) cc_final: 0.9075 (mp) REVERT: G 321 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: H 96 ASP cc_start: 0.5111 (OUTLIER) cc_final: 0.4620 (p0) outliers start: 55 outliers final: 30 residues processed: 354 average time/residue: 0.2893 time to fit residues: 148.6971 Evaluate side-chains 326 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 284 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 129 LEU Chi-restraints excluded: chain A residue 142 PHE 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 324 HIS Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 96 ASP 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 129 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 108 HIS 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 129 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 127 TYR 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 321 GLN Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 204 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 204 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN G 204 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5148 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= 0.197 Angle : 0.786 15.771 21924 Z= 0.380 Chirality : 0.041 0.148 2404 Planarity : 0.003 0.035 2768 Dihedral : 4.054 26.204 2180 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.92 % Allowed : 23.93 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.19), residues: 1936 helix: 1.10 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -1.66 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 288 HIS 0.002 0.001 HIS A 575 PHE 0.027 0.001 PHE H 20 TYR 0.014 0.001 TYR E 100 ARG 0.004 0.000 ARG H 87 *********************** 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 358 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 309 time to evaluate : 1.732 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: A 76 LYS cc_start: 0.6434 (tmtt) cc_final: 0.5840 (mtpp) REVERT: A 142 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: A 237 TYR cc_start: 0.8371 (t80) cc_final: 0.7662 (t80) REVERT: F 73 MET cc_start: -0.0074 (mmt) cc_final: -0.0352 (mtt) REVERT: F 83 GLU cc_start: 0.4830 (tp30) cc_final: 0.3553 (tp30) REVERT: F 96 ASP cc_start: 0.5398 (OUTLIER) cc_final: 0.4907 (p0) REVERT: B 76 LYS cc_start: 0.6424 (tmtt) cc_final: 0.5906 (mtpp) REVERT: B 78 GLN cc_start: 0.7425 (pp30) cc_final: 0.7057 (tt0) REVERT: B 142 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: B 237 TYR cc_start: 0.8521 (t80) cc_final: 0.7969 (t80) REVERT: B 546 MET cc_start: 0.5767 (tpp) cc_final: 0.5281 (tpp) REVERT: C 73 MET cc_start: -0.0312 (mmt) cc_final: -0.0645 (mtt) REVERT: C 83 GLU cc_start: 0.4301 (tp30) cc_final: 0.3246 (tp30) REVERT: C 96 ASP cc_start: 0.5415 (OUTLIER) cc_final: 0.4891 (p0) REVERT: D 76 LYS cc_start: 0.6504 (tmtt) cc_final: 0.6019 (mtpp) REVERT: D 142 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: D 237 TYR cc_start: 0.8522 (t80) cc_final: 0.7977 (t80) REVERT: E 83 GLU cc_start: 0.4289 (tp30) cc_final: 0.3658 (tp30) REVERT: E 96 ASP cc_start: 0.5214 (OUTLIER) cc_final: 0.4649 (p0) REVERT: E 110 MET cc_start: 0.6369 (tpt) cc_final: 0.5864 (tmm) REVERT: G 76 LYS cc_start: 0.6456 (tmtt) cc_final: 0.5882 (mtpp) REVERT: G 142 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: G 237 TYR cc_start: 0.8530 (t80) cc_final: 0.7978 (t80) REVERT: H 73 MET cc_start: -0.0321 (mmt) cc_final: -0.1100 (mtt) REVERT: H 145 MET cc_start: 0.1610 (ppp) cc_final: 0.1103 (ptm) outliers start: 49 outliers final: 27 residues processed: 342 average time/residue: 0.2953 time to fit residues: 144.6097 Evaluate side-chains 324 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 290 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR 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 287 THR 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 96 ASP 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 273 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 142 PHE 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 E residue 45 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 273 ILE 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 45 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 204 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 204 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16256 Z= 0.248 Angle : 0.800 13.864 21924 Z= 0.393 Chirality : 0.043 0.190 2404 Planarity : 0.004 0.041 2768 Dihedral : 4.110 28.473 2180 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.44 % Allowed : 24.46 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 1936 helix: 0.90 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -1.57 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 344 HIS 0.003 0.001 HIS B 575 PHE 0.031 0.002 PHE F 20 TYR 0.019 0.001 TYR H 100 ARG 0.013 0.001 ARG D 332 *********************** 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 342 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 301 time to evaluate : 1.882 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 76 LYS cc_start: 0.6480 (tmtt) cc_final: 0.5851 (mtpp) REVERT: A 142 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: A 237 TYR cc_start: 0.8356 (t80) cc_final: 0.7734 (t80) REVERT: A 546 MET cc_start: 0.5772 (tpp) cc_final: 0.5322 (tpp) REVERT: F 73 MET cc_start: 0.0323 (mmt) cc_final: 0.0007 (mtt) REVERT: F 83 GLU cc_start: 0.4796 (tp30) cc_final: 0.3466 (tp30) REVERT: F 96 ASP cc_start: 0.5492 (OUTLIER) cc_final: 0.4858 (p0) REVERT: B 76 LYS cc_start: 0.6477 (tmtt) cc_final: 0.5887 (mtpp) REVERT: B 78 GLN cc_start: 0.7540 (pp30) cc_final: 0.7181 (tp40) REVERT: B 142 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: B 237 TYR cc_start: 0.8491 (t80) cc_final: 0.7884 (t80) REVERT: B 249 LEU cc_start: 0.9409 (mt) cc_final: 0.9092 (mp) REVERT: B 546 MET cc_start: 0.5816 (tpp) cc_final: 0.5285 (tpp) REVERT: C 83 GLU cc_start: 0.4342 (tp30) cc_final: 0.3695 (tp30) REVERT: C 96 ASP cc_start: 0.5346 (OUTLIER) cc_final: 0.4747 (p0) REVERT: C 110 MET cc_start: 0.6152 (tpt) cc_final: 0.5824 (tmm) REVERT: D 76 LYS cc_start: 0.6592 (tmtt) cc_final: 0.6046 (mtpp) REVERT: D 142 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: D 237 TYR cc_start: 0.8504 (t80) cc_final: 0.7898 (t80) REVERT: D 249 LEU cc_start: 0.9413 (mt) cc_final: 0.9108 (mp) REVERT: E 83 GLU cc_start: 0.4393 (tp30) cc_final: 0.3226 (tp30) REVERT: E 96 ASP cc_start: 0.5447 (OUTLIER) cc_final: 0.4808 (p0) REVERT: E 110 MET cc_start: 0.6607 (tpt) cc_final: 0.6234 (tmm) REVERT: E 116 LYS cc_start: 0.8372 (mptt) cc_final: 0.7490 (mmtm) REVERT: G 76 LYS cc_start: 0.6553 (tmtt) cc_final: 0.5909 (mtpp) REVERT: G 142 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: G 237 TYR cc_start: 0.8498 (t80) cc_final: 0.7898 (t80) REVERT: H 73 MET cc_start: -0.0128 (mmt) cc_final: -0.0451 (mtt) REVERT: H 96 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.4831 (p0) outliers start: 41 outliers final: 31 residues processed: 330 average time/residue: 0.3073 time to fit residues: 144.5132 Evaluate side-chains 316 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 277 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 287 THR 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 96 ASP Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 244 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 E residue 45 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 273 ILE 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 45 THR Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN A 341 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN B 204 GLN C 144 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 204 GLN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN G 204 GLN H 144 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16256 Z= 0.241 Angle : 0.822 14.036 21924 Z= 0.404 Chirality : 0.043 0.183 2404 Planarity : 0.004 0.048 2768 Dihedral : 4.114 28.167 2180 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.50 % Allowed : 24.94 % Favored : 72.56 % 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 (0.18), residues: 1936 helix: 0.84 (0.12), residues: 1560 sheet: None (None), residues: 0 loop : -1.48 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 344 HIS 0.002 0.001 HIS D 260 PHE 0.026 0.002 PHE F 20 TYR 0.016 0.001 TYR H 100 ARG 0.010 0.000 ARG C 107 ********************** 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 323 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 281 time to evaluate : 1.623 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: 0.6439 (tmtt) cc_final: 0.5799 (mtpp) REVERT: A 142 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: A 237 TYR cc_start: 0.8330 (t80) cc_final: 0.7768 (t80) REVERT: A 546 MET cc_start: 0.5761 (tpp) cc_final: 0.5311 (tpp) REVERT: F 96 ASP cc_start: 0.5464 (OUTLIER) cc_final: 0.4840 (p0) REVERT: B 76 LYS cc_start: 0.6476 (tmtt) cc_final: 0.5897 (mtpp) REVERT: B 78 GLN cc_start: 0.7538 (pp30) cc_final: 0.7145 (tp40) REVERT: B 142 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: B 237 TYR cc_start: 0.8484 (t80) cc_final: 0.7854 (t80) REVERT: B 546 MET cc_start: 0.5809 (tpp) cc_final: 0.5254 (tpp) REVERT: C 83 GLU cc_start: 0.4319 (tp30) cc_final: 0.3299 (tp30) REVERT: C 96 ASP cc_start: 0.5606 (OUTLIER) cc_final: 0.4923 (p0) REVERT: D 76 LYS cc_start: 0.6501 (tmtt) cc_final: 0.5969 (mtpp) REVERT: D 142 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: D 237 TYR cc_start: 0.8486 (t80) cc_final: 0.7862 (t80) REVERT: E 83 GLU cc_start: 0.4468 (tp30) cc_final: 0.3860 (tp30) REVERT: E 96 ASP cc_start: 0.5579 (OUTLIER) cc_final: 0.5020 (p0) REVERT: E 110 MET cc_start: 0.6498 (tpt) cc_final: 0.6269 (tmm) REVERT: G 76 LYS cc_start: 0.6540 (tmtt) cc_final: 0.5917 (mtpp) REVERT: G 142 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: G 237 TYR cc_start: 0.8503 (t80) cc_final: 0.7872 (t80) REVERT: H 96 ASP cc_start: 0.5645 (OUTLIER) cc_final: 0.5017 (p0) REVERT: H 110 MET cc_start: 0.6920 (ppp) cc_final: 0.6652 (ppp) REVERT: H 145 MET cc_start: 0.1382 (ppp) cc_final: 0.0820 (ppp) outliers start: 42 outliers final: 34 residues processed: 308 average time/residue: 0.2858 time to fit residues: 127.3635 Evaluate side-chains 312 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 270 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 244 ILE Chi-restraints excluded: chain A residue 287 THR 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 96 ASP Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 244 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 E residue 45 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 273 ILE 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 45 THR Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 133 optimal weight: 0.3980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN F 144 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.211143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.174849 restraints weight = 28480.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.167949 restraints weight = 36485.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163769 restraints weight = 31670.613| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16256 Z= 0.255 Angle : 0.838 16.718 21924 Z= 0.409 Chirality : 0.043 0.183 2404 Planarity : 0.004 0.043 2768 Dihedral : 4.161 26.483 2180 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.86 % Allowed : 24.40 % Favored : 72.74 % 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: 0.52 (0.18), residues: 1936 helix: 0.81 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -1.31 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 344 HIS 0.003 0.001 HIS D 260 PHE 0.026 0.002 PHE H 93 TYR 0.019 0.001 TYR E 100 ARG 0.013 0.001 ARG D 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3283.43 seconds wall clock time: 62 minutes 59.54 seconds (3779.54 seconds total)