Starting phenix.real_space_refine (version: dev) on Sun Feb 19 01:53:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/02_2023/6d7l_7823.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/02_2023/6d7l_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_7823/02_2023/6d7l_7823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/02_2023/6d7l_7823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/02_2023/6d7l_7823.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7l_7823/02_2023/6d7l_7823.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 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-4877/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: 5.32, per 1000 atoms: 0.58 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: 3.58 Conformation dependent library (CDL) restraints added in 1.5 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: 0.32 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: 2.08 Time building geometry restraints manager: 3.81 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 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. 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: 0.690 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: 0.000 Extract box with map and model: 4.360 Check model and map are aligned: 0.130 Process input model: 25.120 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 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 % 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 *********************** 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 : 1.212 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 outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2852 time to fit residues: 150.6831 Evaluate side-chains 223 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4450 ------------------------------------------------------------------------------- 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: 2.9990 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 87 optimal weight: 10.0000 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 177 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9288 Z= 0.225 Angle : 0.747 6.377 12480 Z= 0.385 Chirality : 0.043 0.134 1420 Planarity : 0.004 0.035 1612 Dihedral : 5.663 19.882 1248 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.23), residues: 1128 helix: 0.07 (0.17), residues: 784 sheet: None (None), residues: 0 loop : -4.80 (0.20), residues: 344 *********************** 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 266 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 233 time to evaluate : 1.145 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 outliers start: 33 outliers final: 11 residues processed: 259 average time/residue: 0.2393 time to fit residues: 82.3224 Evaluate side-chains 162 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0893 time to fit residues: 3.3364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 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 75 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5338 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= 0.223 Angle : 0.826 13.392 12480 Z= 0.404 Chirality : 0.045 0.262 1420 Planarity : 0.005 0.064 1612 Dihedral : 5.445 19.409 1248 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 2.56 % 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: -1.49 (0.24), residues: 1128 helix: 0.55 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -4.73 (0.20), residues: 352 *********************** 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 214 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 1.197 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 outliers start: 26 outliers final: 3 residues processed: 205 average time/residue: 0.2079 time to fit residues: 59.8877 Evaluate side-chains 165 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1055 time to fit residues: 2.1749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.7477 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9288 Z= 0.202 Angle : 0.759 11.287 12480 Z= 0.380 Chirality : 0.046 0.341 1420 Planarity : 0.005 0.066 1612 Dihedral : 5.182 18.906 1248 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer Outliers : 1.97 % 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: -1.14 (0.24), residues: 1128 helix: 0.79 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -4.61 (0.21), residues: 348 *********************** 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 201 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 1.236 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 outliers start: 20 outliers final: 9 residues processed: 195 average time/residue: 0.1913 time to fit residues: 54.1212 Evaluate side-chains 156 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1118 time to fit residues: 3.1122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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** ** A 776 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 84 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: 0.7497 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9288 Z= 0.205 Angle : 0.728 11.940 12480 Z= 0.366 Chirality : 0.044 0.281 1420 Planarity : 0.004 0.042 1612 Dihedral : 5.029 18.347 1248 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 1.77 % 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: -0.75 (0.25), residues: 1128 helix: 1.04 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -4.47 (0.22), residues: 340 *********************** 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 192 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 1.316 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 outliers start: 18 outliers final: 7 residues processed: 185 average time/residue: 0.1881 time to fit residues: 50.3585 Evaluate side-chains 162 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0824 time to fit residues: 2.7056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** ** A 776 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 84 ASN ** 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: 0.7596 moved from start: 0.6366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 9288 Z= 0.297 Angle : 0.774 11.393 12480 Z= 0.401 Chirality : 0.045 0.171 1420 Planarity : 0.005 0.037 1612 Dihedral : 5.194 20.155 1248 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer Outliers : 2.36 % 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: -0.54 (0.26), residues: 1128 helix: 1.26 (0.20), residues: 784 sheet: None (None), residues: 0 loop : -4.48 (0.22), residues: 344 *********************** 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 189 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.196 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 outliers start: 24 outliers final: 13 residues processed: 180 average time/residue: 0.1801 time to fit residues: 47.5421 Evaluate side-chains 161 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0957 time to fit residues: 3.6898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 84 ASN ** 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: 0.7551 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9288 Z= 0.211 Angle : 0.789 12.966 12480 Z= 0.402 Chirality : 0.043 0.144 1420 Planarity : 0.004 0.037 1612 Dihedral : 5.049 18.724 1248 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 1.28 % 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: -0.36 (0.26), residues: 1128 helix: 1.46 (0.20), residues: 780 sheet: None (None), residues: 0 loop : -4.52 (0.21), residues: 348 *********************** 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 184 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.061 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 outliers start: 13 outliers final: 5 residues processed: 179 average time/residue: 0.1830 time to fit residues: 47.7150 Evaluate side-chains 152 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0939 time to fit residues: 2.4549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 84 ASN ** 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: 0.7537 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9288 Z= 0.205 Angle : 0.781 13.127 12480 Z= 0.396 Chirality : 0.043 0.157 1420 Planarity : 0.004 0.041 1612 Dihedral : 4.910 17.594 1248 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 1.18 % 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: -0.37 (0.26), residues: 1128 helix: 1.40 (0.20), residues: 784 sheet: None (None), residues: 0 loop : -4.47 (0.22), residues: 344 *********************** 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 183 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.159 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 outliers start: 12 outliers final: 3 residues processed: 175 average time/residue: 0.1860 time to fit residues: 47.4700 Evaluate side-chains 163 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0998 time to fit residues: 1.9089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.0070 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 84 ASN ** 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: 0.7550 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9288 Z= 0.214 Angle : 0.809 13.635 12480 Z= 0.400 Chirality : 0.043 0.142 1420 Planarity : 0.004 0.039 1612 Dihedral : 4.877 17.407 1248 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1128 helix: 1.38 (0.20), residues: 788 sheet: None (None), residues: 0 loop : -4.58 (0.21), residues: 340 *********************** 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 173 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.131 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 outliers start: 8 outliers final: 1 residues processed: 169 average time/residue: 0.1793 time to fit residues: 44.9505 Evaluate side-chains 153 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1164 time to fit residues: 1.6963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 84 ASN C 800 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9288 Z= 0.238 Angle : 0.831 13.637 12480 Z= 0.412 Chirality : 0.044 0.169 1420 Planarity : 0.004 0.036 1612 Dihedral : 4.920 17.987 1248 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 1128 helix: 1.34 (0.20), residues: 788 sheet: None (None), residues: 0 loop : -4.64 (0.21), residues: 340 ********************** 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 155 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 1.182 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 outliers start: 5 outliers final: 2 residues processed: 151 average time/residue: 0.1757 time to fit residues: 39.1908 Evaluate side-chains 151 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1197 time to fit residues: 1.9390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** A 800 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 800 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN C 800 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.098164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.086238 restraints weight = 33705.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.087918 restraints weight = 23697.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.089165 restraints weight = 17891.734| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.7138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9288 Z= 0.248 Angle : 0.836 13.342 12480 Z= 0.414 Chirality : 0.044 0.146 1420 Planarity : 0.004 0.036 1612 Dihedral : 4.992 19.387 1248 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer Outliers : 0.98 % 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: -0.47 (0.26), residues: 1128 helix: 1.38 (0.20), residues: 788 sheet: None (None), residues: 0 loop : -4.69 (0.20), residues: 340 =============================================================================== Job complete usr+sys time: 1837.09 seconds wall clock time: 34 minutes 35.24 seconds (2075.24 seconds total)