Starting phenix.real_space_refine on Thu Mar 14 15:37:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/03_2024/6d7l_7823.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/03_2024/6d7l_7823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/03_2024/6d7l_7823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/03_2024/6d7l_7823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/03_2024/6d7l_7823.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/03_2024/6d7l_7823.pdb" } resolution = 4.0 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= 0.005 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 56 5.16 5 C 5760 2.51 5 N 1584 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 785": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 785": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 785": "NH1" <-> "NH2" Residue "D ARG 815": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9172 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2293 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 2 Chain: "B" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2293 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 2 Chain: "C" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2293 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 2 Chain: "D" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2293 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 2 Time building chain proxies: 5.05, per 1000 atoms: 0.55 Number of scatterers: 9172 At special positions: 0 Unit cell: (108.504, 108.504, 78.912, 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 56 16.00 O 1772 8.00 N 1584 7.00 C 5760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.39 Conformation dependent library (CDL) restraints added in 1.7 seconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 69.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.847A pdb=" N TYR A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.859A pdb=" N VAL A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.604A pdb=" N ALA A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.828A pdb=" N HIS A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.537A pdb=" N VAL A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 182 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.542A pdb=" N LYS A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.567A pdb=" N THR A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.554A pdb=" N GLU A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 796 Processing helix chain 'A' and resid 800 through 823 removed outlier: 3.569A pdb=" N LEU A 804 " --> pdb=" O ASN A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 3.846A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.859A pdb=" N VAL B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 3.605A pdb=" N ALA B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.828A pdb=" N HIS B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.535A pdb=" N VAL B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.541A pdb=" N LYS B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.567A pdb=" N THR B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.554A pdb=" N GLU B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 796 Processing helix chain 'B' and resid 800 through 823 removed outlier: 3.568A pdb=" N LEU B 804 " --> pdb=" O ASN B 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 49 removed outlier: 3.847A pdb=" N TYR C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.860A pdb=" N VAL C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.605A pdb=" N ALA C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.828A pdb=" N HIS C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.536A pdb=" N VAL C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 182 " --> pdb=" O MET C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.541A pdb=" N LYS C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.567A pdb=" N THR C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 292 removed outlier: 3.555A pdb=" N GLU C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 796 Processing helix chain 'C' and resid 800 through 823 removed outlier: 3.569A pdb=" N LEU C 804 " --> pdb=" O ASN C 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 49 removed outlier: 3.846A pdb=" N TYR D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 85 through 94 removed outlier: 3.859A pdb=" N VAL D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.605A pdb=" N ALA D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.827A pdb=" N HIS D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.535A pdb=" N VAL D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS D 182 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.542A pdb=" N LYS D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.566A pdb=" N THR D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 292 removed outlier: 3.555A pdb=" N GLU D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 796 Processing helix chain 'D' and resid 800 through 823 removed outlier: 3.568A pdb=" N LEU D 804 " --> pdb=" O ASN D 800 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1503 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: 2.20 Time building geometry restraints manager: 4.65 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: 3084 1.34 - 1.46: 1532 1.46 - 1.58: 4588 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9288 Sorted by residual: bond pdb=" C SER A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 4.09e+00 bond pdb=" C SER C 158 " pdb=" N PRO C 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 4.09e+00 bond pdb=" C SER D 158 " pdb=" N PRO D 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 4.09e+00 bond pdb=" C SER B 158 " pdb=" N PRO B 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 3.94e+00 bond pdb=" N PRO C 224 " pdb=" CD PRO C 224 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.44e+00 ... (remaining 9283 not shown) Histogram of bond angle deviations from ideal: 100.60 - 106.93: 196 106.93 - 113.25: 5112 113.25 - 119.58: 2750 119.58 - 125.91: 4338 125.91 - 132.24: 84 Bond angle restraints: 12480 Sorted by residual: angle pdb=" C GLU B 232 " pdb=" N ASP B 233 " pdb=" CA ASP B 233 " ideal model delta sigma weight residual 122.83 127.55 -4.72 1.08e+00 8.57e-01 1.91e+01 angle pdb=" C GLU D 232 " pdb=" N ASP D 233 " pdb=" CA ASP D 233 " ideal model delta sigma weight residual 122.83 127.52 -4.69 1.08e+00 8.57e-01 1.89e+01 angle pdb=" C GLU A 232 " pdb=" N ASP A 233 " pdb=" CA ASP A 233 " ideal model delta sigma weight residual 122.83 127.52 -4.69 1.08e+00 8.57e-01 1.89e+01 angle pdb=" C GLU C 232 " pdb=" N ASP C 233 " pdb=" CA ASP C 233 " ideal model delta sigma weight residual 122.83 127.50 -4.67 1.08e+00 8.57e-01 1.87e+01 angle pdb=" N HIS D 124 " pdb=" CA HIS D 124 " pdb=" C HIS D 124 " ideal model delta sigma weight residual 109.81 118.43 -8.62 2.21e+00 2.05e-01 1.52e+01 ... (remaining 12475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.43: 5112 9.43 - 18.85: 644 18.85 - 28.28: 24 28.28 - 37.71: 12 37.71 - 47.14: 12 Dihedral angle restraints: 5804 sinusoidal: 2412 harmonic: 3392 Sorted by residual: dihedral pdb=" CA SER C 158 " pdb=" C SER C 158 " pdb=" N PRO C 159 " pdb=" CA PRO C 159 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER D 158 " pdb=" C SER D 158 " pdb=" N PRO D 159 " pdb=" CA PRO D 159 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER A 158 " pdb=" C SER A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 925 0.044 - 0.088: 382 0.088 - 0.132: 82 0.132 - 0.177: 25 0.177 - 0.221: 6 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA HIS C 124 " pdb=" N HIS C 124 " pdb=" C HIS C 124 " pdb=" CB HIS C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA HIS A 124 " pdb=" N HIS A 124 " pdb=" C HIS A 124 " pdb=" CB HIS A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS B 124 " pdb=" N HIS B 124 " pdb=" C HIS B 124 " pdb=" CB HIS B 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1417 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 158 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 159 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 233 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO D 234 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 234 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 234 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 158 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO C 159 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 159 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 159 " -0.027 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2323 2.80 - 3.32: 8416 3.32 - 3.85: 13449 3.85 - 4.37: 16353 4.37 - 4.90: 26973 Nonbonded interactions: 67514 Sorted by model distance: nonbonded pdb=" O VAL C 82 " pdb=" OH TYR C 114 " model vdw 2.273 2.440 nonbonded pdb=" O VAL B 82 " pdb=" OH TYR B 114 " model vdw 2.273 2.440 nonbonded pdb=" O VAL A 82 " pdb=" OH TYR A 114 " model vdw 2.273 2.440 nonbonded pdb=" O VAL D 82 " pdb=" OH TYR D 114 " model vdw 2.273 2.440 nonbonded pdb=" NZ LYS A 808 " pdb=" OE1 GLU D 806 " model vdw 2.299 2.520 ... (remaining 67509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.680 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: 3.770 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.180 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9288 Z= 0.265 Angle : 0.861 8.617 12480 Z= 0.488 Chirality : 0.052 0.221 1420 Planarity : 0.005 0.048 1612 Dihedral : 7.646 47.136 3596 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.18), residues: 1128 helix: -1.64 (0.14), residues: 780 sheet: None (None), residues: 0 loop : -4.70 (0.21), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 124 PHE 0.010 0.002 PHE A 193 TYR 0.014 0.002 TYR C 218 ARG 0.008 0.001 ARG B 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 0.951 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: A 65 LEU cc_start: 0.7402 (mt) cc_final: 0.6838 (mp) REVERT: A 72 TYR cc_start: 0.6654 (m-80) cc_final: 0.5605 (m-80) REVERT: A 245 LEU cc_start: 0.9360 (mt) cc_final: 0.9144 (mt) REVERT: A 265 GLN cc_start: 0.9335 (mt0) cc_final: 0.9003 (mt0) REVERT: A 793 ASP cc_start: 0.8786 (m-30) cc_final: 0.8451 (t0) REVERT: A 822 LYS cc_start: 0.8562 (mttt) cc_final: 0.8319 (tppt) REVERT: B 65 LEU cc_start: 0.7305 (mt) cc_final: 0.6463 (mp) REVERT: B 72 TYR cc_start: 0.6631 (m-80) cc_final: 0.6130 (m-80) REVERT: B 245 LEU cc_start: 0.9361 (mt) cc_final: 0.9142 (mt) REVERT: B 265 GLN cc_start: 0.9336 (mt0) cc_final: 0.8992 (mt0) REVERT: B 793 ASP cc_start: 0.8783 (m-30) cc_final: 0.8457 (t0) REVERT: C 65 LEU cc_start: 0.7303 (mt) cc_final: 0.6465 (mp) REVERT: C 72 TYR cc_start: 0.6668 (m-80) cc_final: 0.6067 (m-80) REVERT: C 245 LEU cc_start: 0.9382 (mt) cc_final: 0.9163 (mt) REVERT: C 265 GLN cc_start: 0.9345 (mt0) cc_final: 0.9014 (mt0) REVERT: C 793 ASP cc_start: 0.8782 (m-30) cc_final: 0.8428 (t0) REVERT: D 65 LEU cc_start: 0.7403 (mt) cc_final: 0.6835 (mp) REVERT: D 72 TYR cc_start: 0.6656 (m-80) cc_final: 0.6088 (m-80) REVERT: D 245 LEU cc_start: 0.9362 (mt) cc_final: 0.9143 (mt) REVERT: D 265 GLN cc_start: 0.9337 (mt0) cc_final: 0.9004 (mt0) REVERT: D 793 ASP cc_start: 0.8780 (m-30) cc_final: 0.8455 (t0) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2660 time to fit residues: 140.3977 Evaluate side-chains 226 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS A 177 HIS B 66 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS B 177 HIS C 66 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS C 177 HIS D 75 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 177 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9288 Z= 0.218 Angle : 0.731 6.184 12480 Z= 0.377 Chirality : 0.042 0.135 1420 Planarity : 0.005 0.043 1612 Dihedral : 5.681 19.904 1248 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.25 % Allowed : 11.71 % Favored : 85.04 % 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: -2.07 (0.23), residues: 1128 helix: 0.02 (0.17), residues: 784 sheet: None (None), residues: 0 loop : -4.81 (0.20), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 169 PHE 0.006 0.001 PHE A 43 TYR 0.011 0.002 TYR C 192 ARG 0.007 0.001 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 1.210 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 79 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8226 (pp30) REVERT: A 174 GLU cc_start: 0.7048 (tp30) cc_final: 0.6776 (tp30) REVERT: A 245 LEU cc_start: 0.9400 (mt) cc_final: 0.9177 (mt) REVERT: A 265 GLN cc_start: 0.9327 (mt0) cc_final: 0.8995 (mt0) REVERT: A 793 ASP cc_start: 0.8789 (m-30) cc_final: 0.8525 (t0) REVERT: A 795 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8207 (mm-30) REVERT: A 817 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8623 (mt-10) REVERT: A 819 LEU cc_start: 0.9206 (mt) cc_final: 0.8974 (pp) REVERT: B 66 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8753 (p0) REVERT: B 174 GLU cc_start: 0.7056 (tp30) cc_final: 0.6790 (tp30) REVERT: B 245 LEU cc_start: 0.9398 (mt) cc_final: 0.9164 (mt) REVERT: B 265 GLN cc_start: 0.9315 (mt0) cc_final: 0.8941 (mp10) REVERT: B 779 MET cc_start: 0.9232 (tpp) cc_final: 0.8679 (tpp) REVERT: B 793 ASP cc_start: 0.8790 (m-30) cc_final: 0.8526 (t0) REVERT: B 795 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8248 (mm-30) REVERT: B 817 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8589 (mt-10) REVERT: B 821 ASP cc_start: 0.8539 (t0) cc_final: 0.8307 (p0) REVERT: C 66 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8757 (p0) REVERT: C 91 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8375 (mt-10) REVERT: C 174 GLU cc_start: 0.7055 (tp30) cc_final: 0.6789 (tp30) REVERT: C 245 LEU cc_start: 0.9401 (mt) cc_final: 0.9177 (mt) REVERT: C 265 GLN cc_start: 0.9334 (mt0) cc_final: 0.8996 (mt0) REVERT: C 779 MET cc_start: 0.9233 (tpp) cc_final: 0.8673 (tpp) REVERT: C 793 ASP cc_start: 0.8784 (m-30) cc_final: 0.8526 (t0) REVERT: C 795 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8214 (mm-30) REVERT: C 817 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8634 (mt-10) REVERT: C 821 ASP cc_start: 0.8527 (t0) cc_final: 0.8319 (p0) REVERT: D 91 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8442 (mt-10) REVERT: D 174 GLU cc_start: 0.7084 (tp30) cc_final: 0.6864 (tp30) REVERT: D 245 LEU cc_start: 0.9401 (mt) cc_final: 0.9176 (mt) REVERT: D 265 GLN cc_start: 0.9332 (mt0) cc_final: 0.8999 (mt0) REVERT: D 779 MET cc_start: 0.9230 (tpp) cc_final: 0.8679 (tpp) REVERT: D 793 ASP cc_start: 0.8784 (m-30) cc_final: 0.8522 (t0) REVERT: D 795 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8238 (mm-30) REVERT: D 819 LEU cc_start: 0.9148 (mt) cc_final: 0.8883 (pp) outliers start: 33 outliers final: 11 residues processed: 257 average time/residue: 0.2265 time to fit residues: 77.5123 Evaluate side-chains 182 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 0.0070 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9288 Z= 0.218 Angle : 0.779 13.508 12480 Z= 0.382 Chirality : 0.045 0.276 1420 Planarity : 0.005 0.060 1612 Dihedral : 5.441 19.583 1248 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 2.46 % Allowed : 12.80 % Favored : 84.74 % 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: -1.37 (0.24), residues: 1128 helix: 0.62 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -4.74 (0.20), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 169 PHE 0.004 0.001 PHE B 193 TYR 0.012 0.001 TYR A 49 ARG 0.009 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.157 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 91 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: A 174 GLU cc_start: 0.7206 (tp30) cc_final: 0.6628 (tp30) REVERT: A 264 MET cc_start: 0.8908 (mmm) cc_final: 0.8685 (mmm) REVERT: A 265 GLN cc_start: 0.9324 (mt0) cc_final: 0.8621 (mt0) REVERT: A 793 ASP cc_start: 0.8771 (m-30) cc_final: 0.8395 (t0) REVERT: A 795 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8343 (mm-30) REVERT: B 86 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.7098 (p-80) REVERT: B 91 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: B 174 GLU cc_start: 0.7216 (tp30) cc_final: 0.6628 (tp30) REVERT: B 265 GLN cc_start: 0.9307 (mt0) cc_final: 0.8629 (mp10) REVERT: B 793 ASP cc_start: 0.8770 (m-30) cc_final: 0.8408 (t0) REVERT: B 795 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8285 (mm-30) REVERT: C 91 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8444 (mt-10) REVERT: C 174 GLU cc_start: 0.7215 (tp30) cc_final: 0.6640 (tp30) REVERT: C 264 MET cc_start: 0.8908 (mmm) cc_final: 0.8689 (mmm) REVERT: C 265 GLN cc_start: 0.9328 (mt0) cc_final: 0.8628 (mt0) REVERT: C 793 ASP cc_start: 0.8763 (m-30) cc_final: 0.8405 (t0) REVERT: C 795 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8316 (mm-30) REVERT: D 91 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8449 (mt-10) REVERT: D 174 GLU cc_start: 0.7109 (tp30) cc_final: 0.6667 (tp30) REVERT: D 264 MET cc_start: 0.8907 (mmm) cc_final: 0.8689 (mmm) REVERT: D 265 GLN cc_start: 0.9328 (mt0) cc_final: 0.8624 (mt0) REVERT: D 793 ASP cc_start: 0.8766 (m-30) cc_final: 0.8404 (t0) REVERT: D 795 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8343 (mm-30) REVERT: D 819 LEU cc_start: 0.9149 (mt) cc_final: 0.8941 (pp) outliers start: 25 outliers final: 8 residues processed: 216 average time/residue: 0.1892 time to fit residues: 57.3357 Evaluate side-chains 185 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9288 Z= 0.209 Angle : 0.739 11.466 12480 Z= 0.376 Chirality : 0.043 0.232 1420 Planarity : 0.005 0.066 1612 Dihedral : 5.274 19.279 1248 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 1.97 % Allowed : 13.88 % Favored : 84.15 % 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: -1.06 (0.25), residues: 1128 helix: 0.87 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -4.61 (0.21), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 169 PHE 0.004 0.001 PHE A 193 TYR 0.015 0.001 TYR D 72 ARG 0.005 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.106 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 174 GLU cc_start: 0.7310 (tp30) cc_final: 0.6626 (tp30) REVERT: A 265 GLN cc_start: 0.9211 (mt0) cc_final: 0.8915 (mp10) REVERT: A 793 ASP cc_start: 0.8715 (m-30) cc_final: 0.8455 (t0) REVERT: A 795 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8411 (mm-30) REVERT: B 174 GLU cc_start: 0.7312 (tp30) cc_final: 0.6642 (tp30) REVERT: B 265 GLN cc_start: 0.9260 (mt0) cc_final: 0.8959 (mp10) REVERT: B 793 ASP cc_start: 0.8720 (m-30) cc_final: 0.8363 (t0) REVERT: B 795 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8409 (mm-30) REVERT: C 91 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8416 (mt-10) REVERT: C 174 GLU cc_start: 0.7327 (tp30) cc_final: 0.6733 (tp30) REVERT: C 265 GLN cc_start: 0.9216 (mt0) cc_final: 0.8919 (mp10) REVERT: C 793 ASP cc_start: 0.8711 (m-30) cc_final: 0.8362 (t0) REVERT: D 91 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8419 (mt-10) REVERT: D 174 GLU cc_start: 0.7167 (tp30) cc_final: 0.6566 (tp30) REVERT: D 265 GLN cc_start: 0.9216 (mt0) cc_final: 0.8918 (mp10) REVERT: D 793 ASP cc_start: 0.8710 (m-30) cc_final: 0.8456 (t0) REVERT: D 795 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8414 (mm-30) outliers start: 20 outliers final: 15 residues processed: 193 average time/residue: 0.1618 time to fit residues: 46.4006 Evaluate side-chains 173 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 0.0570 chunk 44 optimal weight: 7.9990 chunk 92 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9288 Z= 0.202 Angle : 0.749 11.908 12480 Z= 0.377 Chirality : 0.043 0.210 1420 Planarity : 0.004 0.052 1612 Dihedral : 5.111 18.898 1248 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 2.56 % Allowed : 15.16 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1128 helix: 0.99 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.51 (0.22), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 86 PHE 0.007 0.001 PHE A 193 TYR 0.016 0.001 TYR C 72 ARG 0.006 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 0.898 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 79 GLN cc_start: 0.8564 (tm-30) cc_final: 0.7976 (pp30) REVERT: A 165 ILE cc_start: 0.9417 (mm) cc_final: 0.8885 (tt) REVERT: A 174 GLU cc_start: 0.7286 (tp30) cc_final: 0.6911 (tp30) REVERT: A 265 GLN cc_start: 0.9205 (mt0) cc_final: 0.8924 (mp10) REVERT: A 793 ASP cc_start: 0.8698 (m-30) cc_final: 0.8456 (t0) REVERT: A 794 LYS cc_start: 0.8972 (tptp) cc_final: 0.8432 (tppp) REVERT: B 165 ILE cc_start: 0.9419 (mm) cc_final: 0.8888 (tt) REVERT: B 174 GLU cc_start: 0.7278 (tp30) cc_final: 0.6892 (tp30) REVERT: B 265 GLN cc_start: 0.9239 (mt0) cc_final: 0.8989 (mp10) REVERT: B 278 ARG cc_start: 0.5381 (tpp-160) cc_final: 0.5004 (tpp-160) REVERT: B 793 ASP cc_start: 0.8717 (m-30) cc_final: 0.8452 (t0) REVERT: B 794 LYS cc_start: 0.8968 (tptp) cc_final: 0.8430 (tppp) REVERT: B 810 ASP cc_start: 0.8283 (p0) cc_final: 0.7735 (m-30) REVERT: C 91 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8374 (mt-10) REVERT: C 165 ILE cc_start: 0.9418 (mm) cc_final: 0.8888 (tt) REVERT: C 174 GLU cc_start: 0.7347 (tp30) cc_final: 0.6591 (tp30) REVERT: C 265 GLN cc_start: 0.9220 (mt0) cc_final: 0.8934 (mp10) REVERT: C 278 ARG cc_start: 0.5403 (tpp-160) cc_final: 0.5037 (tpp-160) REVERT: C 793 ASP cc_start: 0.8707 (m-30) cc_final: 0.8456 (t0) REVERT: C 794 LYS cc_start: 0.8950 (tptp) cc_final: 0.8431 (tppp) REVERT: C 810 ASP cc_start: 0.8282 (p0) cc_final: 0.7763 (m-30) REVERT: D 91 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8398 (mt-10) REVERT: D 165 ILE cc_start: 0.9423 (mm) cc_final: 0.8890 (tt) REVERT: D 174 GLU cc_start: 0.7331 (tp30) cc_final: 0.6778 (tp30) REVERT: D 265 GLN cc_start: 0.9212 (mt0) cc_final: 0.8926 (mp10) REVERT: D 278 ARG cc_start: 0.5375 (tpp-160) cc_final: 0.5007 (tpp-160) REVERT: D 793 ASP cc_start: 0.8697 (m-30) cc_final: 0.8457 (t0) REVERT: D 794 LYS cc_start: 0.8969 (tptp) cc_final: 0.8431 (tppp) REVERT: D 810 ASP cc_start: 0.8189 (p0) cc_final: 0.7839 (m-30) outliers start: 26 outliers final: 16 residues processed: 217 average time/residue: 0.1773 time to fit residues: 54.9742 Evaluate side-chains 187 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9288 Z= 0.274 Angle : 0.780 11.884 12480 Z= 0.394 Chirality : 0.045 0.191 1420 Planarity : 0.005 0.044 1612 Dihedral : 5.109 19.351 1248 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 2.95 % Allowed : 18.41 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1128 helix: 1.15 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.43 (0.22), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 124 PHE 0.005 0.001 PHE C 255 TYR 0.012 0.001 TYR D 72 ARG 0.005 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.9469 (mm) cc_final: 0.8974 (tt) REVERT: A 174 GLU cc_start: 0.7275 (tp30) cc_final: 0.6931 (tp30) REVERT: A 265 GLN cc_start: 0.9219 (mt0) cc_final: 0.8944 (mp10) REVERT: A 793 ASP cc_start: 0.8790 (m-30) cc_final: 0.8433 (t0) REVERT: A 810 ASP cc_start: 0.8282 (p0) cc_final: 0.7964 (m-30) REVERT: B 165 ILE cc_start: 0.9471 (mm) cc_final: 0.8975 (tt) REVERT: B 174 GLU cc_start: 0.7286 (tp30) cc_final: 0.6954 (tp30) REVERT: B 265 GLN cc_start: 0.9279 (mt0) cc_final: 0.8995 (mp10) REVERT: B 793 ASP cc_start: 0.8796 (m-30) cc_final: 0.8437 (t0) REVERT: C 91 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8391 (mt-10) REVERT: C 165 ILE cc_start: 0.9472 (mm) cc_final: 0.8976 (tt) REVERT: C 174 GLU cc_start: 0.7318 (tp30) cc_final: 0.6999 (tp30) REVERT: C 265 GLN cc_start: 0.9234 (mt0) cc_final: 0.8955 (mp10) REVERT: C 793 ASP cc_start: 0.8781 (m-30) cc_final: 0.8439 (t0) REVERT: D 91 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8351 (mt-10) REVERT: D 165 ILE cc_start: 0.9477 (mm) cc_final: 0.8976 (tt) REVERT: D 174 GLU cc_start: 0.7335 (tp30) cc_final: 0.6935 (tp30) REVERT: D 265 GLN cc_start: 0.9237 (mt0) cc_final: 0.8957 (mp10) REVERT: D 793 ASP cc_start: 0.8774 (m-30) cc_final: 0.8428 (t0) REVERT: D 810 ASP cc_start: 0.8273 (p0) cc_final: 0.7819 (m-30) outliers start: 30 outliers final: 16 residues processed: 200 average time/residue: 0.1823 time to fit residues: 53.0470 Evaluate side-chains 173 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9288 Z= 0.222 Angle : 0.814 12.429 12480 Z= 0.403 Chirality : 0.046 0.307 1420 Planarity : 0.004 0.038 1612 Dihedral : 5.050 18.811 1248 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.25 % Allowed : 18.11 % Favored : 78.64 % 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: -0.57 (0.25), residues: 1128 helix: 1.29 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -4.56 (0.20), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 169 PHE 0.009 0.001 PHE D 193 TYR 0.012 0.001 TYR D 72 ARG 0.004 0.000 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.094 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 49 TYR cc_start: 0.8305 (m-10) cc_final: 0.8066 (m-10) REVERT: A 79 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8728 (pp30) REVERT: A 91 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: A 165 ILE cc_start: 0.9446 (mm) cc_final: 0.8945 (tt) REVERT: A 174 GLU cc_start: 0.7242 (tp30) cc_final: 0.6848 (tp30) REVERT: A 265 GLN cc_start: 0.9204 (mt0) cc_final: 0.8936 (mp10) REVERT: A 793 ASP cc_start: 0.8721 (m-30) cc_final: 0.8432 (t0) REVERT: A 810 ASP cc_start: 0.8258 (p0) cc_final: 0.8014 (p0) REVERT: B 165 ILE cc_start: 0.9449 (mm) cc_final: 0.8949 (tt) REVERT: B 174 GLU cc_start: 0.7253 (tp30) cc_final: 0.6877 (tp30) REVERT: B 265 GLN cc_start: 0.9252 (mt0) cc_final: 0.9002 (mp10) REVERT: B 793 ASP cc_start: 0.8743 (m-30) cc_final: 0.8440 (t0) REVERT: C 165 ILE cc_start: 0.9449 (mm) cc_final: 0.8950 (tt) REVERT: C 174 GLU cc_start: 0.7275 (tp30) cc_final: 0.6901 (tp30) REVERT: C 265 GLN cc_start: 0.9203 (mt0) cc_final: 0.8940 (mp10) REVERT: C 793 ASP cc_start: 0.8712 (m-30) cc_final: 0.8426 (t0) REVERT: D 91 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8299 (mt-10) REVERT: D 165 ILE cc_start: 0.9452 (mm) cc_final: 0.8950 (tt) REVERT: D 174 GLU cc_start: 0.7313 (tp30) cc_final: 0.6882 (tp30) REVERT: D 265 GLN cc_start: 0.9207 (mt0) cc_final: 0.8940 (mp10) REVERT: D 793 ASP cc_start: 0.8720 (m-30) cc_final: 0.8442 (t0) REVERT: D 810 ASP cc_start: 0.8218 (p0) cc_final: 0.7833 (m-30) outliers start: 33 outliers final: 18 residues processed: 196 average time/residue: 0.1646 time to fit residues: 47.3127 Evaluate side-chains 175 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9288 Z= 0.207 Angle : 0.837 13.332 12480 Z= 0.412 Chirality : 0.047 0.284 1420 Planarity : 0.004 0.036 1612 Dihedral : 4.973 18.036 1248 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 2.07 % Allowed : 18.90 % Favored : 79.04 % 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: -0.66 (0.25), residues: 1128 helix: 1.23 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.67 (0.20), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 86 PHE 0.004 0.001 PHE D 193 TYR 0.018 0.001 TYR A 72 ARG 0.003 0.000 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.9447 (mm) cc_final: 0.8940 (tt) REVERT: A 174 GLU cc_start: 0.7317 (tp30) cc_final: 0.6868 (tp30) REVERT: A 265 GLN cc_start: 0.9190 (mt0) cc_final: 0.8931 (mp10) REVERT: B 165 ILE cc_start: 0.9450 (mm) cc_final: 0.8940 (tt) REVERT: B 174 GLU cc_start: 0.7283 (tp30) cc_final: 0.6535 (tp30) REVERT: B 265 GLN cc_start: 0.9246 (mt0) cc_final: 0.8978 (mp10) REVERT: B 793 ASP cc_start: 0.8738 (m-30) cc_final: 0.8516 (t0) REVERT: C 165 ILE cc_start: 0.9450 (mm) cc_final: 0.8943 (tt) REVERT: C 174 GLU cc_start: 0.7323 (tp30) cc_final: 0.6589 (tp30) REVERT: C 265 GLN cc_start: 0.9203 (mt0) cc_final: 0.8949 (mp10) REVERT: D 91 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8296 (mt-10) REVERT: D 165 ILE cc_start: 0.9453 (mm) cc_final: 0.8943 (tt) REVERT: D 174 GLU cc_start: 0.7305 (tp30) cc_final: 0.6912 (tp30) REVERT: D 265 GLN cc_start: 0.9219 (mt0) cc_final: 0.8963 (mp10) REVERT: D 793 ASP cc_start: 0.8734 (m-30) cc_final: 0.8519 (t0) REVERT: D 810 ASP cc_start: 0.8180 (p0) cc_final: 0.7798 (m-30) outliers start: 21 outliers final: 15 residues processed: 180 average time/residue: 0.1753 time to fit residues: 45.6556 Evaluate side-chains 171 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9288 Z= 0.216 Angle : 0.855 13.588 12480 Z= 0.414 Chirality : 0.048 0.360 1420 Planarity : 0.004 0.035 1612 Dihedral : 4.921 18.907 1248 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 1.77 % Allowed : 20.47 % Favored : 77.76 % 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: -0.60 (0.25), residues: 1128 helix: 1.31 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -4.68 (0.20), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 124 PHE 0.010 0.001 PHE A 193 TYR 0.018 0.001 TYR C 72 ARG 0.003 0.000 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.085 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 165 ILE cc_start: 0.9462 (mm) cc_final: 0.9045 (tt) REVERT: A 174 GLU cc_start: 0.7251 (tp30) cc_final: 0.6838 (tp30) REVERT: B 165 ILE cc_start: 0.9465 (mm) cc_final: 0.9044 (tt) REVERT: B 174 GLU cc_start: 0.7326 (tp30) cc_final: 0.6931 (tp30) REVERT: B 245 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8943 (mt) REVERT: B 265 GLN cc_start: 0.9248 (mt0) cc_final: 0.8990 (mp10) REVERT: B 793 ASP cc_start: 0.8716 (m-30) cc_final: 0.8514 (t0) REVERT: C 165 ILE cc_start: 0.9468 (mm) cc_final: 0.9050 (tt) REVERT: C 174 GLU cc_start: 0.7327 (tp30) cc_final: 0.6970 (tp30) REVERT: D 165 ILE cc_start: 0.9471 (mm) cc_final: 0.9048 (tt) REVERT: D 174 GLU cc_start: 0.7356 (tp30) cc_final: 0.6969 (tp30) REVERT: D 810 ASP cc_start: 0.8197 (p0) cc_final: 0.7806 (m-30) outliers start: 18 outliers final: 16 residues processed: 174 average time/residue: 0.1680 time to fit residues: 42.8905 Evaluate side-chains 169 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9288 Z= 0.211 Angle : 0.856 13.878 12480 Z= 0.413 Chirality : 0.048 0.384 1420 Planarity : 0.004 0.035 1612 Dihedral : 4.877 20.377 1248 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 1.77 % Allowed : 20.87 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1128 helix: 1.35 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -4.68 (0.20), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 86 PHE 0.003 0.001 PHE B 157 TYR 0.019 0.001 TYR A 72 ARG 0.004 0.000 ARG D 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.094 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 58 MET cc_start: 0.8676 (mmm) cc_final: 0.8417 (mtt) REVERT: A 165 ILE cc_start: 0.9466 (mm) cc_final: 0.9046 (tt) REVERT: A 174 GLU cc_start: 0.7212 (tp30) cc_final: 0.6817 (tp30) REVERT: B 165 ILE cc_start: 0.9470 (mm) cc_final: 0.9043 (tt) REVERT: B 174 GLU cc_start: 0.7262 (tp30) cc_final: 0.6898 (tp30) REVERT: B 245 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8909 (mt) REVERT: B 265 GLN cc_start: 0.9244 (mt0) cc_final: 0.8982 (mp10) REVERT: C 165 ILE cc_start: 0.9471 (mm) cc_final: 0.9053 (tt) REVERT: C 174 GLU cc_start: 0.7373 (tp30) cc_final: 0.7058 (tp30) REVERT: D 165 ILE cc_start: 0.9474 (mm) cc_final: 0.9054 (tt) REVERT: D 174 GLU cc_start: 0.7409 (tp30) cc_final: 0.7046 (tp30) REVERT: D 810 ASP cc_start: 0.8256 (p0) cc_final: 0.7882 (m-30) outliers start: 18 outliers final: 16 residues processed: 177 average time/residue: 0.1732 time to fit residues: 44.8284 Evaluate side-chains 171 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.099634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.087437 restraints weight = 33795.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.089237 restraints weight = 23484.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.090522 restraints weight = 17593.248| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9288 Z= 0.211 Angle : 0.853 13.428 12480 Z= 0.413 Chirality : 0.048 0.380 1420 Planarity : 0.004 0.035 1612 Dihedral : 4.849 20.336 1248 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 1.48 % Allowed : 21.26 % Favored : 77.26 % 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 (0.25), residues: 1128 helix: 1.37 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -4.69 (0.20), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 86 PHE 0.009 0.001 PHE D 193 TYR 0.035 0.001 TYR A 49 ARG 0.003 0.000 ARG D 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.06 seconds wall clock time: 34 minutes 41.93 seconds (2081.93 seconds total)