Starting phenix.real_space_refine on Tue Sep 24 23:55:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/09_2024/6osa_20181.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/09_2024/6osa_20181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/09_2024/6osa_20181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/09_2024/6osa_20181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/09_2024/6osa_20181.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osa_20181/09_2024/6osa_20181.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2130 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 4672 2.51 5 N 1256 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7338 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2532 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2585 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 410 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.47, per 1000 atoms: 0.61 Number of scatterers: 7338 At special positions: 0 Unit cell: (78.44, 114.48, 112.36, 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 54 16.00 O 1356 8.00 N 1256 7.00 C 4672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 972.0 milliseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 48.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.987A pdb=" N VAL R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 139 through 171 Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.514A pdb=" N ALA R 176 " --> pdb=" O HIS R 172 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 200 removed outlier: 3.886A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 206 Processing helix chain 'R' and resid 229 through 273 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 280 through 329 removed outlier: 4.211A pdb=" N GLN R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.803A pdb=" N ILE R 329 " --> pdb=" O MET R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 356 removed outlier: 4.025A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 368 removed outlier: 4.141A pdb=" N ILE R 362 " --> pdb=" O THR R 358 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU R 363 " --> pdb=" O ILE R 359 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR R 364 " --> pdb=" O ASN R 360 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 383 removed outlier: 3.593A pdb=" N HIS R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE R 374 " --> pdb=" O ASN R 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.961A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.169A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.563A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.914A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.105A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.733A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.520A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.800A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.644A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.765A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 4.072A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.732A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.348A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.615A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.857A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.261A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.759A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1227 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: 2.19 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2372 1.35 - 1.48: 1912 1.48 - 1.61: 3125 1.61 - 1.74: 0 1.74 - 1.86: 77 Bond restraints: 7486 Sorted by residual: bond pdb=" C LEU R 317 " pdb=" N PRO R 318 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.28e-02 6.10e+03 1.71e+01 bond pdb=" C MET R 120 " pdb=" N PRO R 121 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.20e-02 6.94e+03 1.44e+01 bond pdb=" SD MET B 61 " pdb=" CE MET B 61 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.78e+00 bond pdb=" CG LEU B 51 " pdb=" CD2 LEU B 51 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.37e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.36e+00 ... (remaining 7481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 10002 3.52 - 7.05: 128 7.05 - 10.57: 10 10.57 - 14.10: 3 14.10 - 17.62: 1 Bond angle restraints: 10144 Sorted by residual: angle pdb=" CA LEU R 263 " pdb=" CB LEU R 263 " pdb=" CG LEU R 263 " ideal model delta sigma weight residual 116.30 133.92 -17.62 3.50e+00 8.16e-02 2.54e+01 angle pdb=" C HIS B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 122.08 128.54 -6.46 1.47e+00 4.63e-01 1.93e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 122.07 127.69 -5.62 1.43e+00 4.89e-01 1.55e+01 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 130.04 -13.74 3.50e+00 8.16e-02 1.54e+01 ... (remaining 10139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 4167 16.15 - 32.30: 234 32.30 - 48.45: 40 48.45 - 64.60: 3 64.60 - 80.75: 8 Dihedral angle restraints: 4452 sinusoidal: 1719 harmonic: 2733 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 173.75 -80.75 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE L 12 " pdb=" C ILE L 12 " pdb=" N LEU L 13 " pdb=" CA LEU L 13 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 4449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 826 0.053 - 0.106: 259 0.106 - 0.160: 68 0.160 - 0.213: 14 0.213 - 0.266: 4 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1168 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 243 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C MET R 243 " -0.053 2.00e-02 2.50e+03 pdb=" O MET R 243 " 0.020 2.00e-02 2.50e+03 pdb=" N SER R 244 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 124 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C LEU R 124 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU R 124 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR R 125 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO C 49 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.036 5.00e-02 4.00e+02 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1009 2.75 - 3.29: 6844 3.29 - 3.82: 12240 3.82 - 4.36: 13986 4.36 - 4.90: 24939 Nonbonded interactions: 59018 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.309 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.319 3.040 nonbonded pdb=" O GLY B 182 " pdb=" NZ LYS B 209 " model vdw 2.329 3.120 nonbonded pdb=" O LEU R 94 " pdb=" NE2 GLN R 98 " model vdw 2.335 3.120 ... (remaining 59013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 : 0.008 0.093 7486 Z= 0.554 Angle : 1.075 17.625 10144 Z= 0.593 Chirality : 0.058 0.266 1171 Planarity : 0.007 0.065 1277 Dihedral : 11.086 75.182 2674 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: -2.75 (0.23), residues: 921 helix: -1.70 (0.20), residues: 414 sheet: -0.85 (0.39), residues: 169 loop : -2.31 (0.27), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP B 99 HIS 0.028 0.004 HIS B 142 PHE 0.042 0.004 PHE B 180 TYR 0.032 0.004 TYR R 354 ARG 0.015 0.001 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.848 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 91 LYS cc_start: 0.7132 (mttt) cc_final: 0.6903 (mmmm) REVERT: R 237 ILE cc_start: 0.8094 (mt) cc_final: 0.7812 (mp) REVERT: R 325 MET cc_start: 0.6473 (mmt) cc_final: 0.5754 (pp-130) REVERT: A 6 SER cc_start: 0.6884 (m) cc_final: 0.6495 (p) REVERT: A 208 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7707 (ttp-110) REVERT: A 245 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 280 LYS cc_start: 0.8342 (mppt) cc_final: 0.7870 (mtmt) REVERT: B 12 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7360 (tp30) REVERT: B 175 GLN cc_start: 0.8375 (mm110) cc_final: 0.8051 (mm-40) REVERT: B 264 TYR cc_start: 0.8458 (m-80) cc_final: 0.8162 (m-80) REVERT: C 19 LEU cc_start: 0.8978 (mt) cc_final: 0.8771 (mt) REVERT: C 27 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7970 (mtt-85) outliers start: 0 outliers final: 2 residues processed: 218 average time/residue: 1.1888 time to fit residues: 273.1491 Evaluate side-chains 136 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 HIS R 238 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN R 320 HIS R 365 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 259 GLN B 268 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7486 Z= 0.222 Angle : 0.653 10.247 10144 Z= 0.343 Chirality : 0.043 0.156 1171 Planarity : 0.005 0.041 1277 Dihedral : 5.534 51.468 1013 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.51 % Allowed : 14.91 % Favored : 80.58 % 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: -0.79 (0.25), residues: 921 helix: 0.49 (0.24), residues: 432 sheet: -0.36 (0.39), residues: 148 loop : -1.89 (0.29), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.008 0.001 HIS B 142 PHE 0.011 0.001 PHE B 292 TYR 0.022 0.002 TYR A 290 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 246 ILE cc_start: 0.8202 (mm) cc_final: 0.7980 (mm) REVERT: R 325 MET cc_start: 0.6346 (mmt) cc_final: 0.5867 (pp-130) REVERT: A 52 GLN cc_start: 0.7514 (mt0) cc_final: 0.7187 (mp10) REVERT: A 208 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7440 (ttp-110) REVERT: A 269 ASN cc_start: 0.8961 (m110) cc_final: 0.8727 (m110) REVERT: A 280 LYS cc_start: 0.8214 (mppt) cc_final: 0.7769 (mtmm) REVERT: A 281 SER cc_start: 0.8671 (m) cc_final: 0.8245 (p) REVERT: A 310 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8459 (tt) REVERT: B 12 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7679 (tp30) REVERT: B 74 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8323 (t) REVERT: B 175 GLN cc_start: 0.8308 (mm110) cc_final: 0.7999 (mm-40) REVERT: B 217 MET cc_start: 0.7839 (pmm) cc_final: 0.7595 (pmm) outliers start: 36 outliers final: 11 residues processed: 169 average time/residue: 1.0597 time to fit residues: 190.0940 Evaluate side-chains 129 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 304 GLN B 75 GLN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7486 Z= 0.200 Angle : 0.598 9.300 10144 Z= 0.312 Chirality : 0.042 0.161 1171 Planarity : 0.004 0.058 1277 Dihedral : 5.082 50.325 1013 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.76 % Allowed : 17.29 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.27), residues: 921 helix: 1.39 (0.25), residues: 427 sheet: -0.29 (0.38), residues: 158 loop : -1.59 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.011 0.001 HIS B 142 PHE 0.011 0.001 PHE R 345 TYR 0.017 0.002 TYR R 339 ARG 0.011 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 325 MET cc_start: 0.6286 (mmt) cc_final: 0.6041 (pp-130) REVERT: A 52 GLN cc_start: 0.7562 (mt0) cc_final: 0.7263 (mp10) REVERT: A 280 LYS cc_start: 0.8260 (mppt) cc_final: 0.7867 (mppt) REVERT: A 281 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8205 (p) REVERT: A 313 ARG cc_start: 0.7700 (ptp-110) cc_final: 0.7481 (ptp-170) REVERT: B 12 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7610 (tp30) REVERT: B 23 LYS cc_start: 0.7726 (tppp) cc_final: 0.7358 (tptp) REVERT: B 154 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: B 175 GLN cc_start: 0.8250 (mm110) cc_final: 0.7909 (mm-40) REVERT: B 217 MET cc_start: 0.7847 (pmm) cc_final: 0.7604 (pmm) outliers start: 38 outliers final: 18 residues processed: 145 average time/residue: 1.0377 time to fit residues: 159.9590 Evaluate side-chains 129 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.0040 chunk 42 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7486 Z= 0.186 Angle : 0.593 10.352 10144 Z= 0.306 Chirality : 0.042 0.174 1171 Planarity : 0.004 0.060 1277 Dihedral : 4.800 48.190 1011 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.64 % Allowed : 19.05 % Favored : 76.32 % 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: 0.43 (0.27), residues: 921 helix: 1.84 (0.25), residues: 421 sheet: -0.45 (0.37), residues: 171 loop : -1.37 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE R 375 TYR 0.014 0.002 TYR R 339 ARG 0.013 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 48 THR cc_start: 0.8761 (m) cc_final: 0.8484 (t) REVERT: A 247 MET cc_start: 0.8604 (mtm) cc_final: 0.8305 (mtp) REVERT: A 280 LYS cc_start: 0.8290 (mppt) cc_final: 0.7888 (mppt) REVERT: A 281 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8219 (p) REVERT: A 310 LEU cc_start: 0.8853 (mt) cc_final: 0.8617 (tt) REVERT: A 313 ARG cc_start: 0.7724 (ptp-110) cc_final: 0.7476 (ptp-170) REVERT: B 12 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7470 (tp30) REVERT: B 175 GLN cc_start: 0.8246 (mm110) cc_final: 0.7903 (mm-40) REVERT: B 217 MET cc_start: 0.7759 (pmm) cc_final: 0.7419 (pmm) REVERT: B 234 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.9004 (m-80) outliers start: 37 outliers final: 18 residues processed: 152 average time/residue: 0.9837 time to fit residues: 159.4581 Evaluate side-chains 131 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 304 GLN B 237 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7486 Z= 0.193 Angle : 0.596 11.517 10144 Z= 0.304 Chirality : 0.041 0.159 1171 Planarity : 0.004 0.062 1277 Dihedral : 4.714 47.212 1011 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.26 % Allowed : 20.05 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.28), residues: 921 helix: 2.02 (0.25), residues: 420 sheet: -0.43 (0.37), residues: 174 loop : -1.28 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS R 343 PHE 0.011 0.001 PHE R 375 TYR 0.015 0.002 TYR R 339 ARG 0.014 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 118 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 247 MET cc_start: 0.8608 (mtm) cc_final: 0.8302 (mtp) REVERT: A 261 ASP cc_start: 0.7710 (t70) cc_final: 0.7288 (t0) REVERT: A 280 LYS cc_start: 0.8278 (mppt) cc_final: 0.7885 (mppt) REVERT: A 281 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8261 (p) REVERT: A 310 LEU cc_start: 0.8831 (mt) cc_final: 0.8621 (tt) REVERT: B 12 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7575 (tp30) REVERT: B 154 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8142 (m-30) REVERT: B 163 ASP cc_start: 0.8324 (p0) cc_final: 0.8110 (p0) REVERT: B 175 GLN cc_start: 0.8229 (mm110) cc_final: 0.7949 (mm110) REVERT: B 217 MET cc_start: 0.7882 (pmm) cc_final: 0.7565 (pmm) REVERT: B 234 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.9003 (m-80) REVERT: B 280 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7668 (ttmt) outliers start: 42 outliers final: 20 residues processed: 146 average time/residue: 1.0646 time to fit residues: 165.1864 Evaluate side-chains 132 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 0.0040 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 343 HIS R 373 HIS A 52 GLN A 304 GLN B 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7486 Z= 0.156 Angle : 0.569 9.371 10144 Z= 0.292 Chirality : 0.041 0.163 1171 Planarity : 0.004 0.064 1277 Dihedral : 4.385 43.642 1009 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.76 % Allowed : 20.80 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 921 helix: 2.11 (0.25), residues: 425 sheet: -0.30 (0.37), residues: 171 loop : -1.28 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE R 375 TYR 0.014 0.001 TYR R 339 ARG 0.017 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7696 (t70) cc_final: 0.7278 (t0) REVERT: A 280 LYS cc_start: 0.8299 (mppt) cc_final: 0.7863 (mtmt) REVERT: A 281 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8320 (p) REVERT: B 12 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7558 (tp30) REVERT: B 124 TYR cc_start: 0.8453 (m-80) cc_final: 0.8065 (m-80) REVERT: B 175 GLN cc_start: 0.8208 (mm110) cc_final: 0.7934 (mm110) REVERT: B 217 MET cc_start: 0.7823 (pmm) cc_final: 0.7582 (pmm) REVERT: B 234 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8937 (m-80) REVERT: C 20 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8755 (mtmm) outliers start: 38 outliers final: 14 residues processed: 151 average time/residue: 1.1231 time to fit residues: 179.9174 Evaluate side-chains 127 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 GLN A 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7486 Z= 0.293 Angle : 0.655 12.786 10144 Z= 0.333 Chirality : 0.043 0.163 1171 Planarity : 0.004 0.073 1277 Dihedral : 4.666 48.827 1009 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.51 % Allowed : 22.68 % Favored : 72.81 % 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: 0.59 (0.28), residues: 921 helix: 1.95 (0.25), residues: 423 sheet: -0.49 (0.37), residues: 171 loop : -1.19 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.014 0.002 PHE R 345 TYR 0.018 0.002 TYR R 339 ARG 0.017 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 153 TYR cc_start: 0.8479 (m-80) cc_final: 0.8173 (m-80) REVERT: A 261 ASP cc_start: 0.7722 (t70) cc_final: 0.7332 (t0) REVERT: A 280 LYS cc_start: 0.8354 (mppt) cc_final: 0.7935 (mppt) REVERT: A 281 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8358 (p) REVERT: A 304 GLN cc_start: 0.7989 (tt0) cc_final: 0.7706 (mt0) REVERT: B 12 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7544 (tp30) REVERT: B 175 GLN cc_start: 0.8236 (mm110) cc_final: 0.7924 (mm-40) REVERT: B 217 MET cc_start: 0.7730 (pmm) cc_final: 0.7465 (pmm) REVERT: B 234 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.9036 (m-80) REVERT: B 323 ASP cc_start: 0.7645 (t0) cc_final: 0.7387 (t0) REVERT: C 18 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7949 (mm-40) outliers start: 36 outliers final: 22 residues processed: 137 average time/residue: 1.1195 time to fit residues: 163.8877 Evaluate side-chains 133 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 182 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 HIS A 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7486 Z= 0.190 Angle : 0.615 12.139 10144 Z= 0.314 Chirality : 0.041 0.164 1171 Planarity : 0.004 0.074 1277 Dihedral : 4.528 46.982 1009 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.14 % Allowed : 22.93 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.28), residues: 921 helix: 2.02 (0.25), residues: 427 sheet: -0.49 (0.37), residues: 174 loop : -1.33 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 320 PHE 0.023 0.001 PHE R 375 TYR 0.015 0.002 TYR R 339 ARG 0.018 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 153 TYR cc_start: 0.8438 (m-80) cc_final: 0.8222 (m-80) REVERT: A 261 ASP cc_start: 0.7675 (t70) cc_final: 0.7297 (t0) REVERT: A 280 LYS cc_start: 0.8323 (mppt) cc_final: 0.7918 (mppt) REVERT: A 281 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 304 GLN cc_start: 0.7911 (tt0) cc_final: 0.7663 (mt0) REVERT: B 12 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7534 (tp30) REVERT: B 23 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7947 (ttmm) REVERT: B 124 TYR cc_start: 0.8557 (m-80) cc_final: 0.8154 (m-80) REVERT: B 175 GLN cc_start: 0.8203 (mm110) cc_final: 0.7931 (mm110) REVERT: B 217 MET cc_start: 0.7674 (pmm) cc_final: 0.7428 (pmm) REVERT: B 234 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8987 (m-80) REVERT: C 18 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7931 (mm-40) REVERT: C 20 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8775 (mtmm) outliers start: 33 outliers final: 20 residues processed: 134 average time/residue: 1.1757 time to fit residues: 167.2391 Evaluate side-chains 131 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7486 Z= 0.206 Angle : 0.618 12.273 10144 Z= 0.315 Chirality : 0.041 0.163 1171 Planarity : 0.004 0.081 1277 Dihedral : 4.541 47.985 1009 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.76 % Allowed : 23.93 % Favored : 72.31 % 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: 0.69 (0.28), residues: 921 helix: 2.08 (0.25), residues: 427 sheet: -0.36 (0.37), residues: 168 loop : -1.31 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.017 0.001 PHE R 375 TYR 0.033 0.002 TYR A 290 ARG 0.019 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 261 ASP cc_start: 0.7663 (t70) cc_final: 0.7296 (t0) REVERT: A 280 LYS cc_start: 0.8335 (mppt) cc_final: 0.7897 (mtmt) REVERT: A 281 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8375 (p) REVERT: A 304 GLN cc_start: 0.7875 (tt0) cc_final: 0.7646 (mt0) REVERT: A 313 ARG cc_start: 0.7754 (ptp-110) cc_final: 0.7474 (ptp-170) REVERT: B 12 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7500 (tp30) REVERT: B 23 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8000 (ttmm) REVERT: B 175 GLN cc_start: 0.8204 (mm110) cc_final: 0.7895 (mm-40) REVERT: B 217 MET cc_start: 0.7670 (pmm) cc_final: 0.7450 (pmm) REVERT: B 234 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8987 (m-80) REVERT: C 18 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7926 (mm-40) outliers start: 30 outliers final: 22 residues processed: 130 average time/residue: 1.0716 time to fit residues: 148.0633 Evaluate side-chains 130 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7486 Z= 0.196 Angle : 0.639 13.323 10144 Z= 0.321 Chirality : 0.041 0.186 1171 Planarity : 0.004 0.083 1277 Dihedral : 4.506 47.261 1009 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.38 % Allowed : 24.31 % Favored : 72.31 % 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: 0.72 (0.28), residues: 921 helix: 2.15 (0.25), residues: 426 sheet: -0.48 (0.38), residues: 170 loop : -1.27 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.001 PHE R 375 TYR 0.015 0.001 TYR R 339 ARG 0.019 0.001 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 261 ASP cc_start: 0.7656 (t70) cc_final: 0.7274 (t0) REVERT: A 280 LYS cc_start: 0.8337 (mppt) cc_final: 0.7898 (mtmt) REVERT: A 281 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8408 (p) REVERT: A 304 GLN cc_start: 0.7857 (tt0) cc_final: 0.7636 (mt0) REVERT: A 313 ARG cc_start: 0.7692 (ptp-110) cc_final: 0.7439 (ptp-170) REVERT: B 12 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7490 (tp30) REVERT: B 175 GLN cc_start: 0.8201 (mm110) cc_final: 0.7886 (mm-40) REVERT: B 217 MET cc_start: 0.7662 (pmm) cc_final: 0.7432 (pmm) REVERT: B 234 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8978 (m-80) REVERT: C 18 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7908 (mm-40) REVERT: C 20 LYS cc_start: 0.9135 (ttmm) cc_final: 0.8763 (mtmm) REVERT: C 21 MET cc_start: 0.8173 (tmt) cc_final: 0.7922 (tmt) outliers start: 27 outliers final: 20 residues processed: 134 average time/residue: 1.0721 time to fit residues: 152.6857 Evaluate side-chains 126 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105955 restraints weight = 10831.996| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.47 r_work: 0.3248 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7486 Z= 0.307 Angle : 0.686 12.626 10144 Z= 0.350 Chirality : 0.044 0.222 1171 Planarity : 0.005 0.086 1277 Dihedral : 4.777 50.042 1009 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.26 % Allowed : 24.81 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 921 helix: 2.01 (0.25), residues: 427 sheet: -0.43 (0.39), residues: 163 loop : -1.28 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.014 0.002 PHE R 375 TYR 0.035 0.002 TYR A 290 ARG 0.020 0.001 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3311.45 seconds wall clock time: 58 minutes 36.28 seconds (3516.28 seconds total)