Starting phenix.real_space_refine on Sat Aug 3 06:39:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/08_2024/8wu1_37849.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/08_2024/8wu1_37849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/08_2024/8wu1_37849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/08_2024/8wu1_37849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/08_2024/8wu1_37849.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/08_2024/8wu1_37849.cif" } resolution = 3.2 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= 0.001 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 31 5.16 5 C 4648 2.51 5 N 1226 2.21 5 O 1338 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7250 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2577 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 330} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 176 Chain: "H" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1314 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "L" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1191 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "R" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2139 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain breaks: 3 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Classifications: {'peptide': 1} Time building chain proxies: 4.86, per 1000 atoms: 0.67 Number of scatterers: 7250 At special positions: 0 Unit cell: (151.59, 102.3, 88.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 6 15.00 F 1 9.00 O 1338 8.00 N 1226 7.00 C 4648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 15 sheets defined 26.2% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'C' and resid 98 through 108 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.894A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.039A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'L' and resid 183 through 187 removed outlier: 3.944A pdb=" N TYR L 187 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 141 removed outlier: 4.100A pdb=" N LEU R 117 " --> pdb=" O PRO R 113 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 150 removed outlier: 4.021A pdb=" N CYS R 149 " --> pdb=" O ARG R 145 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG R 150 " --> pdb=" O SER R 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 145 through 150' Processing helix chain 'R' and resid 150 through 179 Processing helix chain 'R' and resid 187 through 220 Processing helix chain 'R' and resid 222 through 228 removed outlier: 4.034A pdb=" N ARG R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 250 Processing helix chain 'R' and resid 251 through 253 No H-bonds generated for 'chain 'R' and resid 251 through 253' Processing helix chain 'R' and resid 273 through 309 Processing helix chain 'R' and resid 340 through 369 Proline residue: R 358 - end of helix removed outlier: 3.556A pdb=" N ALA R 361 " --> pdb=" O GLY R 357 " (cutoff:3.500A) Processing helix chain 'R' and resid 374 through 399 Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 401 through 408 Processing sheet with id=AA1, first strand: chain 'C' and resid 112 through 117 Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 87 removed outlier: 7.217A pdb=" N LEU C 79 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N PHE C 61 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 81 " --> pdb=" O CYS C 59 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N CYS C 59 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU C 57 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C 55 " --> pdb=" O GLN C 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 188 removed outlier: 3.769A pdb=" N SER C 202 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 209 removed outlier: 3.527A pdb=" N PHE C 349 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 8 through 10 Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.419A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.419A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 133 removed outlier: 5.878A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER H 187 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA H 178 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER H 189 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.509A pdb=" N LYS H 219 " --> pdb=" O CYS H 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB4, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.515A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.515A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.536A pdb=" N THR L 181 " --> pdb=" O ASN L 159 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN L 159 " --> pdb=" O THR L 181 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1068 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: 2.44 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1123 1.31 - 1.43: 1950 1.43 - 1.56: 4269 1.56 - 1.68: 26 1.68 - 1.81: 39 Bond restraints: 7407 Sorted by residual: bond pdb=" CAX KCA R 501 " pdb=" CBC KCA R 501 " ideal model delta sigma weight residual 1.399 1.577 -0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" CAY KCA R 501 " pdb=" CAZ KCA R 501 " ideal model delta sigma weight residual 1.402 1.579 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" CAV KCA R 501 " pdb=" CAW KCA R 501 " ideal model delta sigma weight residual 1.385 1.545 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" CAS KCA R 501 " pdb=" CAT KCA R 501 " ideal model delta sigma weight residual 1.380 1.534 -0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" CAR KCA R 501 " pdb=" CAS KCA R 501 " ideal model delta sigma weight residual 1.389 1.542 -0.153 2.00e-02 2.50e+03 5.85e+01 ... (remaining 7402 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.15: 257 107.15 - 113.88: 4330 113.88 - 120.60: 2735 120.60 - 127.33: 2747 127.33 - 134.06: 88 Bond angle restraints: 10157 Sorted by residual: angle pdb=" CB TPO R 432 " pdb=" OG1 TPO R 432 " pdb=" P TPO R 432 " ideal model delta sigma weight residual 119.31 107.40 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CB TPO R 431 " pdb=" OG1 TPO R 431 " pdb=" P TPO R 431 " ideal model delta sigma weight residual 119.31 108.34 10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C TYR L 141 " pdb=" N PRO L 142 " pdb=" CD PRO L 142 " ideal model delta sigma weight residual 120.60 112.66 7.94 2.20e+00 2.07e-01 1.30e+01 angle pdb=" OG1 TPO R 431 " pdb=" P TPO R 431 " pdb=" O1P TPO R 431 " ideal model delta sigma weight residual 100.43 109.61 -9.18 3.00e+00 1.11e-01 9.37e+00 angle pdb=" OG1 TPO R 432 " pdb=" P TPO R 432 " pdb=" O1P TPO R 432 " ideal model delta sigma weight residual 100.43 109.58 -9.15 3.00e+00 1.11e-01 9.29e+00 ... (remaining 10152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 4014 15.82 - 31.63: 279 31.63 - 47.44: 62 47.44 - 63.26: 13 63.26 - 79.07: 2 Dihedral angle restraints: 4370 sinusoidal: 1406 harmonic: 2964 Sorted by residual: dihedral pdb=" CB CYS R 257 " pdb=" SG CYS R 257 " pdb=" SG CYS R 264 " pdb=" CB CYS R 264 " ideal model delta sinusoidal sigma weight residual -86.00 -117.12 31.12 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CA PHE R 268 " pdb=" C PHE R 268 " pdb=" N PRO R 269 " pdb=" CA PRO R 269 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ASP C 260 " pdb=" CB ASP C 260 " pdb=" CG ASP C 260 " pdb=" OD1 ASP C 260 " ideal model delta sinusoidal sigma weight residual -30.00 -81.28 51.28 1 2.00e+01 2.50e-03 8.99e+00 ... (remaining 4367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 918 0.040 - 0.080: 220 0.080 - 0.121: 87 0.121 - 0.161: 16 0.161 - 0.201: 1 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CB THR R 344 " pdb=" CA THR R 344 " pdb=" OG1 THR R 344 " pdb=" CG2 THR R 344 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA KCA R 501 " pdb=" N KCA R 501 " pdb=" C KCA R 501 " pdb=" CB KCA R 501 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA VAL H 40 " pdb=" N VAL H 40 " pdb=" C VAL H 40 " pdb=" CB VAL H 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1239 not shown) Planarity restraints: 1266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 141 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.85e+01 pdb=" N PRO L 142 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO L 142 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO L 142 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 350 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C VAL R 350 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL R 350 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL R 351 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 80 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO L 81 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 81 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 81 " -0.026 5.00e-02 4.00e+02 ... (remaining 1263 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 827 2.75 - 3.28: 7065 3.28 - 3.82: 11395 3.82 - 4.36: 12689 4.36 - 4.90: 22904 Nonbonded interactions: 54880 Sorted by model distance: nonbonded pdb=" NZ LYS L 40 " pdb=" O GLU L 82 " model vdw 2.208 3.120 nonbonded pdb=" OD1 ASP R 272 " pdb=" N GLU R 273 " model vdw 2.226 3.120 nonbonded pdb=" NE2 GLN C 130 " pdb=" O ARG C 282 " model vdw 2.243 3.120 nonbonded pdb=" OD1 ASP C 240 " pdb=" NE2 GLN C 248 " model vdw 2.259 3.120 nonbonded pdb=" OG SER R 265 " pdb=" O PHE R 268 " model vdw 2.267 3.040 ... (remaining 54875 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=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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.850 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 0.178 7407 Z= 0.494 Angle : 0.621 11.908 10157 Z= 0.306 Chirality : 0.043 0.201 1242 Planarity : 0.005 0.107 1266 Dihedral : 11.916 79.075 2439 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.27), residues: 981 helix: 0.96 (0.33), residues: 248 sheet: -0.60 (0.28), residues: 318 loop : -0.93 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 279 HIS 0.010 0.001 HIS C 353 PHE 0.016 0.001 PHE H 105 TYR 0.015 0.001 TYR H 107 ARG 0.008 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.853 Fit side-chains REVERT: C 160 LYS cc_start: 0.8117 (tmmt) cc_final: 0.7331 (tppt) REVERT: R 214 ARG cc_start: 0.7229 (mtp180) cc_final: 0.6929 (mpt180) REVERT: R 400 ARG cc_start: 0.7038 (mmm160) cc_final: 0.6135 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2195 time to fit residues: 38.7895 Evaluate side-chains 119 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7407 Z= 0.214 Angle : 0.566 9.109 10157 Z= 0.290 Chirality : 0.043 0.153 1242 Planarity : 0.004 0.070 1266 Dihedral : 5.595 66.064 1104 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.59 % Allowed : 7.20 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.28 (0.27), residues: 981 helix: 1.12 (0.33), residues: 233 sheet: -0.28 (0.29), residues: 315 loop : -0.75 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 279 HIS 0.004 0.001 HIS C 353 PHE 0.021 0.002 PHE H 105 TYR 0.019 0.001 TYR H 107 ARG 0.005 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.847 Fit side-chains REVERT: C 160 LYS cc_start: 0.8271 (tmmt) cc_final: 0.7527 (tppt) outliers start: 11 outliers final: 8 residues processed: 132 average time/residue: 0.1981 time to fit residues: 34.8933 Evaluate side-chains 127 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 302 HIS Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7407 Z= 0.260 Angle : 0.557 8.249 10157 Z= 0.287 Chirality : 0.043 0.162 1242 Planarity : 0.004 0.056 1266 Dihedral : 5.589 63.547 1104 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.45 % Allowed : 10.37 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.22 (0.27), residues: 981 helix: 0.89 (0.33), residues: 239 sheet: -0.16 (0.29), residues: 312 loop : -0.61 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 279 HIS 0.006 0.001 HIS C 353 PHE 0.024 0.002 PHE H 105 TYR 0.018 0.001 TYR H 107 ARG 0.005 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.863 Fit side-chains REVERT: C 160 LYS cc_start: 0.8310 (tmmt) cc_final: 0.7606 (tppt) REVERT: R 400 ARG cc_start: 0.7122 (mmm160) cc_final: 0.6782 (mmt180) outliers start: 17 outliers final: 10 residues processed: 124 average time/residue: 0.2035 time to fit residues: 33.6197 Evaluate side-chains 125 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7407 Z= 0.362 Angle : 0.601 9.332 10157 Z= 0.310 Chirality : 0.044 0.160 1242 Planarity : 0.004 0.061 1266 Dihedral : 5.808 64.426 1104 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.31 % Allowed : 11.82 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.25 (0.27), residues: 981 helix: 0.87 (0.34), residues: 239 sheet: -0.14 (0.29), residues: 314 loop : -0.67 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 279 HIS 0.007 0.001 HIS C 353 PHE 0.032 0.002 PHE H 105 TYR 0.022 0.002 TYR H 107 ARG 0.006 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 0.917 Fit side-chains REVERT: C 160 LYS cc_start: 0.8451 (tmmt) cc_final: 0.7793 (tppt) REVERT: L 31 SER cc_start: 0.8589 (p) cc_final: 0.8331 (p) REVERT: R 209 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8836 (mm) REVERT: R 247 ILE cc_start: 0.7967 (mm) cc_final: 0.7523 (mt) REVERT: R 400 ARG cc_start: 0.7289 (mmm160) cc_final: 0.6282 (tmt-80) outliers start: 23 outliers final: 17 residues processed: 131 average time/residue: 0.2117 time to fit residues: 36.6825 Evaluate side-chains 133 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 167 GLN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.0010 chunk 86 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7407 Z= 0.204 Angle : 0.546 9.191 10157 Z= 0.278 Chirality : 0.042 0.162 1242 Planarity : 0.004 0.061 1266 Dihedral : 5.544 65.012 1104 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.59 % Allowed : 14.12 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: 981 helix: 1.09 (0.34), residues: 239 sheet: -0.01 (0.29), residues: 300 loop : -0.59 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 279 HIS 0.004 0.001 HIS C 353 PHE 0.020 0.001 PHE H 105 TYR 0.017 0.001 TYR H 107 ARG 0.008 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.800 Fit side-chains REVERT: C 160 LYS cc_start: 0.8300 (tmmt) cc_final: 0.7653 (tppt) REVERT: R 209 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8854 (mm) REVERT: R 247 ILE cc_start: 0.7920 (mm) cc_final: 0.7447 (mt) REVERT: R 376 LYS cc_start: 0.6394 (ttmt) cc_final: 0.6002 (ttpt) REVERT: R 400 ARG cc_start: 0.7189 (mmm160) cc_final: 0.6343 (tmt-80) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.2350 time to fit residues: 40.7878 Evaluate side-chains 132 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7407 Z= 0.284 Angle : 0.563 9.468 10157 Z= 0.289 Chirality : 0.043 0.174 1242 Planarity : 0.004 0.063 1266 Dihedral : 5.614 67.539 1104 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.59 % Allowed : 15.42 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.07 (0.27), residues: 981 helix: 0.99 (0.34), residues: 240 sheet: -0.02 (0.29), residues: 318 loop : -0.57 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 279 HIS 0.006 0.001 HIS C 353 PHE 0.026 0.002 PHE H 105 TYR 0.019 0.001 TYR R 296 ARG 0.012 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.859 Fit side-chains REVERT: C 160 LYS cc_start: 0.8289 (tmmt) cc_final: 0.7683 (tppt) REVERT: R 129 PHE cc_start: 0.7116 (t80) cc_final: 0.6712 (t80) REVERT: R 209 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8877 (mm) REVERT: R 376 LYS cc_start: 0.6363 (ttmt) cc_final: 0.6014 (ttpt) REVERT: R 400 ARG cc_start: 0.7271 (mmm160) cc_final: 0.6361 (tmt-80) outliers start: 18 outliers final: 17 residues processed: 126 average time/residue: 0.2129 time to fit residues: 35.3808 Evaluate side-chains 133 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.0170 chunk 81 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 0.0040 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.5430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7407 Z= 0.161 Angle : 0.522 9.749 10157 Z= 0.266 Chirality : 0.041 0.160 1242 Planarity : 0.004 0.064 1266 Dihedral : 5.323 66.924 1104 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.87 % Allowed : 16.57 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 981 helix: 1.11 (0.34), residues: 240 sheet: 0.25 (0.30), residues: 298 loop : -0.60 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 279 HIS 0.003 0.001 HIS C 353 PHE 0.021 0.001 PHE H 156 TYR 0.017 0.001 TYR R 296 ARG 0.009 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.862 Fit side-chains REVERT: C 160 LYS cc_start: 0.8207 (tmmt) cc_final: 0.7565 (tppt) REVERT: R 129 PHE cc_start: 0.7133 (t80) cc_final: 0.6741 (t80) REVERT: R 209 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8897 (mm) REVERT: R 376 LYS cc_start: 0.6406 (ttmt) cc_final: 0.6054 (ttpt) REVERT: R 400 ARG cc_start: 0.7253 (mmm160) cc_final: 0.6421 (tmt-80) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 0.2106 time to fit residues: 36.5591 Evaluate side-chains 129 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 0.1980 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7407 Z= 0.418 Angle : 0.615 9.447 10157 Z= 0.319 Chirality : 0.044 0.172 1242 Planarity : 0.005 0.069 1266 Dihedral : 5.821 71.768 1104 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.88 % Allowed : 16.57 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.09 (0.27), residues: 981 helix: 0.87 (0.34), residues: 240 sheet: -0.02 (0.29), residues: 323 loop : -0.52 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 106 HIS 0.007 0.001 HIS C 353 PHE 0.034 0.002 PHE H 105 TYR 0.022 0.002 TYR H 107 ARG 0.002 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: C 160 LYS cc_start: 0.8367 (tmmt) cc_final: 0.7797 (tppt) REVERT: C 240 ASP cc_start: 0.7992 (m-30) cc_final: 0.7624 (m-30) REVERT: R 209 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8888 (mm) REVERT: R 400 ARG cc_start: 0.7394 (mmm160) cc_final: 0.6435 (tmt-80) outliers start: 20 outliers final: 16 residues processed: 129 average time/residue: 0.2053 time to fit residues: 34.9550 Evaluate side-chains 133 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.0070 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.0570 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7407 Z= 0.148 Angle : 0.545 9.535 10157 Z= 0.274 Chirality : 0.041 0.150 1242 Planarity : 0.004 0.065 1266 Dihedral : 5.365 69.679 1104 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.44 % Allowed : 18.44 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: 0.16 (0.27), residues: 981 helix: 1.10 (0.34), residues: 240 sheet: 0.35 (0.30), residues: 292 loop : -0.54 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 279 HIS 0.003 0.001 HIS C 111 PHE 0.019 0.001 PHE H 156 TYR 0.020 0.001 TYR R 296 ARG 0.009 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.894 Fit side-chains REVERT: C 160 LYS cc_start: 0.8253 (tmmt) cc_final: 0.7698 (tppt) REVERT: R 129 PHE cc_start: 0.7111 (t80) cc_final: 0.6749 (t80) REVERT: R 209 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8844 (mm) REVERT: R 376 LYS cc_start: 0.6404 (ttmt) cc_final: 0.6071 (ttpt) REVERT: R 400 ARG cc_start: 0.7299 (mmm160) cc_final: 0.6411 (tmt-80) outliers start: 10 outliers final: 7 residues processed: 124 average time/residue: 0.2063 time to fit residues: 34.0375 Evaluate side-chains 124 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7407 Z= 0.216 Angle : 0.556 9.756 10157 Z= 0.283 Chirality : 0.042 0.159 1242 Planarity : 0.004 0.070 1266 Dihedral : 5.395 70.610 1104 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.15 % Allowed : 19.45 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: 0.16 (0.27), residues: 981 helix: 1.03 (0.34), residues: 240 sheet: 0.37 (0.30), residues: 299 loop : -0.52 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 279 HIS 0.004 0.001 HIS C 353 PHE 0.020 0.001 PHE R 191 TYR 0.027 0.001 TYR R 296 ARG 0.006 0.000 ARG R 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.825 Fit side-chains REVERT: C 160 LYS cc_start: 0.8277 (tmmt) cc_final: 0.7742 (tppt) REVERT: R 209 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8882 (mm) REVERT: R 296 TYR cc_start: 0.7365 (t80) cc_final: 0.7089 (t80) REVERT: R 376 LYS cc_start: 0.6518 (ttmt) cc_final: 0.6164 (ttpt) REVERT: R 400 ARG cc_start: 0.7351 (mmm160) cc_final: 0.6397 (tmt-80) outliers start: 8 outliers final: 7 residues processed: 126 average time/residue: 0.2034 time to fit residues: 34.0299 Evaluate side-chains 127 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 391 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 0.0030 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 50.0000 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** 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 = 0.4133 r_free = 0.4133 target = 0.177893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117758 restraints weight = 9796.035| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.01 r_work: 0.3283 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7407 Z= 0.149 Angle : 0.546 9.930 10157 Z= 0.276 Chirality : 0.042 0.154 1242 Planarity : 0.004 0.066 1266 Dihedral : 5.205 69.048 1104 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.15 % Allowed : 20.03 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: 0.29 (0.27), residues: 981 helix: 1.12 (0.34), residues: 240 sheet: 0.50 (0.30), residues: 293 loop : -0.46 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 279 HIS 0.003 0.001 HIS C 111 PHE 0.018 0.001 PHE R 191 TYR 0.020 0.001 TYR R 296 ARG 0.006 0.000 ARG R 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.83 seconds wall clock time: 35 minutes 5.12 seconds (2105.12 seconds total)