Starting phenix.real_space_refine on Tue Feb 13 19:39:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejc_31158/02_2024/7ejc_31158_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejc_31158/02_2024/7ejc_31158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejc_31158/02_2024/7ejc_31158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejc_31158/02_2024/7ejc_31158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejc_31158/02_2024/7ejc_31158_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejc_31158/02_2024/7ejc_31158_updated.pdb" } resolution = 2.97 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= 0.001 sd= 0.012 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: 7 Type Number sf(0) Gaussians Br 6 7.06 5 P 18 5.49 5 Mg 3 5.21 5 S 42 5.16 5 C 4644 2.51 5 N 1302 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7485 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'J46': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'ANP': 2, 'J46': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ANP': 1, 'J46': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.48, per 1000 atoms: 0.60 Number of scatterers: 7485 At special positions: 0 Unit cell: (107.97, 70.8, 110.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 6 34.99 S 42 16.00 P 18 15.00 Mg 3 11.99 O 1470 8.00 N 1302 7.00 C 4644 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 3 sheets defined 41.6% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 69 through 81 Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.565A pdb=" N ARG A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.681A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 197 through 213 removed outlier: 4.003A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.266A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 Processing helix chain 'A' and resid 289 through 295 removed outlier: 4.029A pdb=" N HIS A 294 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 69 through 81 Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.565A pdb=" N ARG C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 135 through 143 removed outlier: 3.680A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 197 through 213 removed outlier: 4.003A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.267A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 259 Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.029A pdb=" N HIS C 294 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 69 through 81 Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.565A pdb=" N ARG B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.680A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 197 through 213 removed outlier: 4.003A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.265A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 259 Processing helix chain 'B' and resid 289 through 295 removed outlier: 4.029A pdb=" N HIS B 294 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.560A pdb=" N ILE A 311 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 263 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N MET A 125 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 265 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 190 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP A 161 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA A 192 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.559A pdb=" N ILE C 311 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 263 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N MET C 125 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 265 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL C 221 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 160 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA C 190 " --> pdb=" O TYR C 159 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP C 161 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA C 192 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.560A pdb=" N ILE B 311 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 263 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N MET B 125 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 265 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA B 190 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP B 161 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA B 192 " --> pdb=" O ASP B 161 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 747 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: 1.95 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2496 1.34 - 1.48: 1724 1.48 - 1.61: 3312 1.61 - 1.74: 9 1.74 - 1.87: 72 Bond restraints: 7613 Sorted by residual: bond pdb=" O3A ANP B 401 " pdb=" PB ANP B 401 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" O3A ANP C 403 " pdb=" PB ANP C 403 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C04 J46 C 404 " pdb=" C07 J46 C 404 " ideal model delta sigma weight residual 1.391 1.529 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C04 J46 A 602 " pdb=" C07 J46 A 602 " ideal model delta sigma weight residual 1.391 1.529 -0.138 2.00e-02 2.50e+03 4.73e+01 ... (remaining 7608 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.18: 214 106.18 - 112.74: 3979 112.74 - 119.29: 2237 119.29 - 125.85: 3819 125.85 - 132.41: 76 Bond angle restraints: 10325 Sorted by residual: angle pdb=" O01 J46 A 602 " pdb=" S01 J46 A 602 " pdb=" O02 J46 A 602 " ideal model delta sigma weight residual 119.86 100.15 19.71 3.00e+00 1.11e-01 4.32e+01 angle pdb=" O01 J46 B 403 " pdb=" S01 J46 B 403 " pdb=" O02 J46 B 403 " ideal model delta sigma weight residual 119.86 100.18 19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" O01 J46 C 404 " pdb=" S01 J46 C 404 " pdb=" O02 J46 C 404 " ideal model delta sigma weight residual 119.86 100.18 19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" N GLY C 236 " pdb=" CA GLY C 236 " pdb=" C GLY C 236 " ideal model delta sigma weight residual 114.69 107.61 7.08 1.19e+00 7.06e-01 3.54e+01 angle pdb=" N GLY B 236 " pdb=" CA GLY B 236 " pdb=" C GLY B 236 " ideal model delta sigma weight residual 114.69 107.67 7.02 1.19e+00 7.06e-01 3.48e+01 ... (remaining 10320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 4283 24.42 - 48.85: 312 48.85 - 73.27: 34 73.27 - 97.69: 6 97.69 - 122.12: 3 Dihedral angle restraints: 4638 sinusoidal: 1986 harmonic: 2652 Sorted by residual: dihedral pdb=" CA ASN A 188 " pdb=" C ASN A 188 " pdb=" N VAL A 189 " pdb=" CA VAL A 189 " ideal model delta harmonic sigma weight residual -180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASN C 188 " pdb=" C ASN C 188 " pdb=" N VAL C 189 " pdb=" CA VAL C 189 " ideal model delta harmonic sigma weight residual 180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ASN B 188 " pdb=" C ASN B 188 " pdb=" N VAL B 189 " pdb=" CA VAL B 189 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 950 0.059 - 0.119: 180 0.119 - 0.178: 28 0.178 - 0.238: 3 0.238 - 0.297: 3 Chirality restraints: 1164 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C3' ANP B 401 " pdb=" C2' ANP B 401 " pdb=" C4' ANP B 401 " pdb=" O3' ANP B 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' ANP C 403 " pdb=" C2' ANP C 403 " pdb=" C4' ANP C 403 " pdb=" O3' ANP C 403 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1161 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 58 " -0.012 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C LYS B 58 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS B 58 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU B 59 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 58 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LYS A 58 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS A 58 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A 59 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 285 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 286 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 286 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 286 " 0.028 5.00e-02 4.00e+02 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 21 2.27 - 2.93: 3279 2.93 - 3.59: 10726 3.59 - 4.24: 18199 4.24 - 4.90: 30460 Nonbonded interactions: 62685 Sorted by model distance: nonbonded pdb=" OG1 THR A 134 " pdb="MG MG A 601 " model vdw 1.616 2.170 nonbonded pdb=" OG1 THR C 134 " pdb="MG MG C 402 " model vdw 1.617 2.170 nonbonded pdb=" OG1 THR B 134 " pdb=" OD2 ASP B 222 " model vdw 1.862 2.440 nonbonded pdb=" OG1 THR C 134 " pdb=" O2B ANP C 401 " model vdw 1.896 2.440 nonbonded pdb=" OG1 THR A 134 " pdb=" O2B ANP B 401 " model vdw 1.946 2.440 ... (remaining 62680 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' and resid 22 through 338) selection = (chain 'B' and resid 22 through 338) selection = (chain 'C' and resid 22 through 338) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 12.780 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.080 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.011 0.144 7613 Z= 0.731 Angle : 1.183 19.709 10325 Z= 0.662 Chirality : 0.049 0.297 1164 Planarity : 0.004 0.051 1290 Dihedral : 16.421 122.115 2940 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % Rotamer: Outliers : 4.17 % Allowed : 5.38 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -3.39 (0.22), residues: 918 helix: -2.04 (0.20), residues: 417 sheet: -1.38 (0.36), residues: 168 loop : -2.77 (0.26), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 294 PHE 0.006 0.001 PHE B 126 TYR 0.020 0.002 TYR B 315 ARG 0.006 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 0.874 Fit side-chains REVERT: A 34 ASN cc_start: 0.8335 (t0) cc_final: 0.8001 (t0) REVERT: A 163 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7677 (mm-30) REVERT: C 68 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7083 (tm-30) REVERT: C 210 MET cc_start: 0.8817 (mtp) cc_final: 0.8588 (mtp) REVERT: B 68 GLU cc_start: 0.7777 (tm-30) cc_final: 0.6987 (tm-30) REVERT: B 198 ASP cc_start: 0.8725 (m-30) cc_final: 0.8523 (m-30) outliers start: 31 outliers final: 5 residues processed: 128 average time/residue: 1.5157 time to fit residues: 202.8784 Evaluate side-chains 67 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain B residue 134 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 34 ASN A 138 HIS ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 330 ASN C 30 GLN C 93 HIS C 138 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN C 330 ASN B 30 GLN B 93 HIS B 138 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 330 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7613 Z= 0.183 Angle : 0.589 7.401 10325 Z= 0.326 Chirality : 0.040 0.128 1164 Planarity : 0.004 0.040 1290 Dihedral : 12.881 106.425 1252 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.55 % Allowed : 15.19 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -1.85 (0.25), residues: 918 helix: -0.43 (0.25), residues: 405 sheet: -0.98 (0.36), residues: 156 loop : -2.20 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 294 PHE 0.007 0.001 PHE A 248 TYR 0.014 0.001 TYR A 315 ARG 0.007 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.8865 (m-30) cc_final: 0.8585 (m-30) REVERT: A 322 GLU cc_start: 0.8330 (tt0) cc_final: 0.7935 (tp30) REVERT: A 326 MET cc_start: 0.8620 (ttp) cc_final: 0.8384 (ttp) REVERT: C 322 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: C 326 MET cc_start: 0.8363 (ttm) cc_final: 0.7956 (ttp) outliers start: 19 outliers final: 8 residues processed: 90 average time/residue: 1.2370 time to fit residues: 117.9193 Evaluate side-chains 76 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.0470 chunk 68 optimal weight: 2.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7613 Z= 0.149 Angle : 0.541 7.506 10325 Z= 0.296 Chirality : 0.039 0.135 1164 Planarity : 0.003 0.033 1290 Dihedral : 10.492 72.847 1246 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.55 % Allowed : 16.26 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -1.28 (0.27), residues: 918 helix: 0.27 (0.26), residues: 411 sheet: -1.21 (0.36), residues: 165 loop : -1.97 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 294 PHE 0.007 0.001 PHE C 126 TYR 0.010 0.001 TYR A 315 ARG 0.005 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8182 (t0) cc_final: 0.7962 (t0) REVERT: A 39 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8576 (mppt) REVERT: A 43 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: A 223 SER cc_start: 0.8010 (m) cc_final: 0.7789 (p) REVERT: A 322 GLU cc_start: 0.8381 (tt0) cc_final: 0.8064 (tp30) REVERT: A 326 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8336 (ttp) REVERT: C 39 LYS cc_start: 0.9014 (mppt) cc_final: 0.8677 (mmtm) REVERT: C 322 GLU cc_start: 0.8268 (tt0) cc_final: 0.8063 (tp30) REVERT: B 43 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: B 218 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8644 (pt) REVERT: B 223 SER cc_start: 0.7903 (m) cc_final: 0.7565 (p) outliers start: 19 outliers final: 6 residues processed: 88 average time/residue: 1.1980 time to fit residues: 111.9844 Evaluate side-chains 78 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.0570 chunk 40 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 202 GLN C 188 ASN C 196 ASN B 196 ASN B 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7613 Z= 0.225 Angle : 0.581 7.616 10325 Z= 0.317 Chirality : 0.041 0.125 1164 Planarity : 0.003 0.038 1290 Dihedral : 10.658 61.149 1245 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 2.82 % Allowed : 17.74 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.90 (0.28), residues: 918 helix: 0.49 (0.26), residues: 411 sheet: -0.71 (0.39), residues: 165 loop : -1.83 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 294 PHE 0.007 0.001 PHE C 327 TYR 0.018 0.001 TYR A 315 ARG 0.004 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8599 (mppt) REVERT: A 43 GLU cc_start: 0.8530 (mp0) cc_final: 0.8187 (mt-10) REVERT: A 184 ASP cc_start: 0.8845 (m-30) cc_final: 0.8487 (m-30) REVERT: A 326 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8259 (ttp) REVERT: C 39 LYS cc_start: 0.9032 (mppt) cc_final: 0.8675 (mmtm) REVERT: C 184 ASP cc_start: 0.8947 (m-30) cc_final: 0.8651 (m-30) REVERT: C 322 GLU cc_start: 0.8336 (tt0) cc_final: 0.7996 (tp30) REVERT: B 43 GLU cc_start: 0.8551 (mp0) cc_final: 0.8220 (mt-10) REVERT: B 184 ASP cc_start: 0.8893 (m-30) cc_final: 0.8559 (m-30) REVERT: B 218 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8746 (pt) outliers start: 21 outliers final: 6 residues processed: 82 average time/residue: 1.1621 time to fit residues: 101.4388 Evaluate side-chains 75 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7613 Z= 0.232 Angle : 0.570 7.613 10325 Z= 0.314 Chirality : 0.041 0.173 1164 Planarity : 0.004 0.037 1290 Dihedral : 10.839 63.881 1245 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.02 % Allowed : 19.89 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.67 (0.28), residues: 918 helix: 0.52 (0.26), residues: 417 sheet: -0.45 (0.41), residues: 162 loop : -1.57 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 294 PHE 0.008 0.001 PHE C 126 TYR 0.017 0.001 TYR A 315 ARG 0.003 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8613 (mppt) REVERT: A 43 GLU cc_start: 0.8531 (mp0) cc_final: 0.8156 (mt-10) REVERT: A 326 MET cc_start: 0.8502 (ttp) cc_final: 0.8207 (ttp) REVERT: C 39 LYS cc_start: 0.9060 (mppt) cc_final: 0.8606 (mmtm) REVERT: C 43 GLU cc_start: 0.8524 (mp0) cc_final: 0.8145 (mt-10) REVERT: C 184 ASP cc_start: 0.8951 (m-30) cc_final: 0.8645 (m-30) REVERT: C 322 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: B 43 GLU cc_start: 0.8512 (mp0) cc_final: 0.8177 (mt-10) REVERT: B 189 VAL cc_start: 0.7327 (OUTLIER) cc_final: 0.7110 (m) REVERT: B 223 SER cc_start: 0.7885 (m) cc_final: 0.7503 (p) outliers start: 15 outliers final: 7 residues processed: 79 average time/residue: 1.2672 time to fit residues: 106.0617 Evaluate side-chains 75 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 0.0370 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7613 Z= 0.175 Angle : 0.545 7.615 10325 Z= 0.299 Chirality : 0.040 0.145 1164 Planarity : 0.003 0.037 1290 Dihedral : 10.652 61.648 1245 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.88 % Allowed : 21.37 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.28), residues: 918 helix: 0.66 (0.26), residues: 417 sheet: -0.42 (0.42), residues: 162 loop : -1.48 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 294 PHE 0.007 0.001 PHE C 126 TYR 0.014 0.001 TYR C 315 ARG 0.011 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8626 (mppt) REVERT: A 43 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8177 (mt-10) REVERT: A 223 SER cc_start: 0.8119 (m) cc_final: 0.7834 (p) REVERT: A 326 MET cc_start: 0.8502 (ttp) cc_final: 0.8196 (ttp) REVERT: C 43 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8115 (mt-10) REVERT: C 322 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: B 43 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8162 (mt-10) REVERT: B 218 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8795 (pt) REVERT: B 223 SER cc_start: 0.7777 (m) cc_final: 0.7385 (p) REVERT: B 306 ARG cc_start: 0.7592 (mmp-170) cc_final: 0.7385 (mmp-170) outliers start: 14 outliers final: 5 residues processed: 77 average time/residue: 1.2166 time to fit residues: 99.5050 Evaluate side-chains 68 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 0.0030 chunk 76 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7613 Z= 0.227 Angle : 0.569 7.740 10325 Z= 0.313 Chirality : 0.041 0.136 1164 Planarity : 0.003 0.032 1290 Dihedral : 10.842 65.010 1245 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % Rotamer: Outliers : 2.28 % Allowed : 21.24 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.28), residues: 918 helix: 0.65 (0.26), residues: 417 sheet: -0.37 (0.42), residues: 165 loop : -1.37 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 294 PHE 0.008 0.001 PHE C 126 TYR 0.018 0.001 TYR A 315 ARG 0.008 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.852 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: A 43 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8173 (mt-10) REVERT: A 223 SER cc_start: 0.8215 (m) cc_final: 0.7916 (p) REVERT: A 326 MET cc_start: 0.8491 (ttp) cc_final: 0.8173 (ttp) REVERT: C 43 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8115 (mt-10) REVERT: C 322 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: B 43 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8134 (mt-10) REVERT: B 223 SER cc_start: 0.7833 (m) cc_final: 0.7416 (p) outliers start: 17 outliers final: 11 residues processed: 74 average time/residue: 1.3337 time to fit residues: 104.3900 Evaluate side-chains 73 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 291 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0020 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7613 Z= 0.144 Angle : 0.533 7.723 10325 Z= 0.291 Chirality : 0.039 0.120 1164 Planarity : 0.003 0.027 1290 Dihedral : 10.402 56.724 1245 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.75 % Allowed : 22.04 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.27 (0.28), residues: 918 helix: 0.80 (0.27), residues: 417 sheet: -0.17 (0.43), residues: 159 loop : -1.35 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 294 PHE 0.006 0.001 PHE C 126 TYR 0.008 0.001 TYR C 315 ARG 0.008 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.863 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: A 43 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8192 (mt-10) REVERT: A 84 MET cc_start: 0.9042 (mtm) cc_final: 0.6316 (tmt) REVERT: A 223 SER cc_start: 0.8128 (m) cc_final: 0.7840 (p) REVERT: A 322 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7970 (tp30) REVERT: A 326 MET cc_start: 0.8495 (ttp) cc_final: 0.8194 (ttp) REVERT: C 43 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8087 (mt-10) REVERT: C 322 GLU cc_start: 0.8352 (tt0) cc_final: 0.8072 (tp30) REVERT: B 43 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8131 (mt-10) REVERT: B 223 SER cc_start: 0.7795 (m) cc_final: 0.7394 (p) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 1.2612 time to fit residues: 114.8675 Evaluate side-chains 78 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 77 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.0060 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN B 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7613 Z= 0.149 Angle : 0.541 7.848 10325 Z= 0.294 Chirality : 0.039 0.117 1164 Planarity : 0.003 0.027 1290 Dihedral : 10.223 55.447 1245 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.61 % Allowed : 23.39 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.16 (0.28), residues: 918 helix: 0.88 (0.26), residues: 417 sheet: -0.05 (0.44), residues: 156 loop : -1.31 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 294 PHE 0.008 0.001 PHE C 126 TYR 0.011 0.001 TYR B 315 ARG 0.008 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 184 ASP cc_start: 0.8811 (m-30) cc_final: 0.8484 (m-30) REVERT: A 213 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 223 SER cc_start: 0.8137 (m) cc_final: 0.7837 (p) REVERT: A 322 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: A 326 MET cc_start: 0.8471 (ttp) cc_final: 0.8192 (ttp) REVERT: C 43 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8095 (mt-10) REVERT: C 322 GLU cc_start: 0.8344 (tt0) cc_final: 0.8057 (tp30) REVERT: B 43 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8136 (mt-10) REVERT: B 223 SER cc_start: 0.7825 (m) cc_final: 0.7413 (p) outliers start: 12 outliers final: 8 residues processed: 79 average time/residue: 1.1941 time to fit residues: 100.1391 Evaluate side-chains 80 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 77 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN B 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7613 Z= 0.204 Angle : 0.574 7.871 10325 Z= 0.312 Chirality : 0.040 0.121 1164 Planarity : 0.003 0.031 1290 Dihedral : 10.535 61.506 1245 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.34 % Allowed : 23.52 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.17 (0.28), residues: 918 helix: 0.85 (0.26), residues: 417 sheet: -0.09 (0.43), residues: 159 loop : -1.27 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 294 PHE 0.007 0.001 PHE C 126 TYR 0.017 0.001 TYR A 315 ARG 0.007 0.000 ARG C 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8150 (mt-10) REVERT: A 184 ASP cc_start: 0.8854 (m-30) cc_final: 0.8524 (m-30) REVERT: A 213 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 223 SER cc_start: 0.8149 (m) cc_final: 0.7855 (p) REVERT: A 322 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: A 326 MET cc_start: 0.8479 (ttp) cc_final: 0.8180 (ttp) REVERT: C 43 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 322 GLU cc_start: 0.8371 (tt0) cc_final: 0.8011 (tp30) REVERT: B 43 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 223 SER cc_start: 0.7813 (m) cc_final: 0.7412 (p) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 1.3589 time to fit residues: 105.0176 Evaluate side-chains 73 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 77 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.066148 restraints weight = 13124.208| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.17 r_work: 0.2782 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7613 Z= 0.189 Angle : 0.570 7.852 10325 Z= 0.309 Chirality : 0.040 0.122 1164 Planarity : 0.003 0.039 1290 Dihedral : 10.534 60.993 1245 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.34 % Allowed : 23.79 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -0.12 (0.28), residues: 918 helix: 0.87 (0.26), residues: 417 sheet: -0.06 (0.43), residues: 159 loop : -1.22 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 294 PHE 0.008 0.001 PHE C 126 TYR 0.014 0.001 TYR A 315 ARG 0.007 0.000 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.45 seconds wall clock time: 49 minutes 38.08 seconds (2978.08 seconds total)