Starting phenix.real_space_refine on Wed Sep 17 14:18:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k2x_36842/09_2025/8k2x_36842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k2x_36842/09_2025/8k2x_36842.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/cci-nas-00/data/ceres_data/8k2x_36842/09_2025/8k2x_36842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k2x_36842/09_2025/8k2x_36842.map" model { file = "/net/cci-nas-00/data/ceres_data/8k2x_36842/09_2025/8k2x_36842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k2x_36842/09_2025/8k2x_36842.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5665 2.51 5 N 1534 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8900 Number of models: 1 Model: "" Number of chains: 7 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: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "R" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2266 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.06, per 1000 atoms: 0.23 Number of scatterers: 8900 At special positions: 0 Unit cell: (90.95, 121.55, 129.2, 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 63 16.00 O 1638 8.00 N 1534 7.00 C 5665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 0.91 Conformation dependent library (CDL) restraints added in 323.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 38.1% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.570A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.603A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.949A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.688A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 48 through 81 Proline residue: R 57 - end of helix removed outlier: 3.642A pdb=" N ALA R 75 " --> pdb=" O ASN R 71 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 106 Processing helix chain 'R' and resid 106 through 111 Processing helix chain 'R' and resid 120 through 154 Processing helix chain 'R' and resid 155 through 163 Processing helix chain 'R' and resid 166 through 190 removed outlier: 3.568A pdb=" N LEU R 170 " --> pdb=" O ALA R 166 " (cutoff:3.500A) Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 208 through 245 Proline residue: R 227 - end of helix Processing helix chain 'R' and resid 249 through 285 Proline residue: R 270 - end of helix removed outlier: 4.568A pdb=" N LEU R 283 " --> pdb=" O ILE R 279 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 319 removed outlier: 3.979A pdb=" N GLU R 293 " --> pdb=" O ASN R 289 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER R 294 " --> pdb=" O CYS R 290 " (cutoff:3.500A) Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 322 through 336 removed outlier: 3.557A pdb=" N LEU R 336 " --> pdb=" O LEU R 332 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.163A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.768A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.630A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.893A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.584A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.025A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.978A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.665A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.944A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.951A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2425 1.33 - 1.46: 1904 1.46 - 1.58: 4662 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 9081 Sorted by residual: bond pdb=" N ASN R 199 " pdb=" CA ASN R 199 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.78e+00 bond pdb=" N LEU L 3 " pdb=" CA LEU L 3 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.60e+00 bond pdb=" N VAL S 149 " pdb=" CA VAL S 149 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.19e-02 7.06e+03 6.26e+00 bond pdb=" N VAL S 147 " pdb=" CA VAL S 147 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.23e-02 6.61e+03 5.49e+00 bond pdb=" N GLU B 172 " pdb=" CA GLU B 172 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.37e+00 ... (remaining 9076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12091 1.88 - 3.75: 179 3.75 - 5.63: 25 5.63 - 7.51: 7 7.51 - 9.38: 2 Bond angle restraints: 12304 Sorted by residual: angle pdb=" C PRO S 148 " pdb=" N VAL S 149 " pdb=" CA VAL S 149 " ideal model delta sigma weight residual 122.71 117.97 4.74 1.44e+00 4.82e-01 1.08e+01 angle pdb=" C PRO S 148 " pdb=" CA PRO S 148 " pdb=" CB PRO S 148 " ideal model delta sigma weight residual 111.56 108.13 3.43 1.09e+00 8.42e-01 9.90e+00 angle pdb=" CA MET R 281 " pdb=" CB MET R 281 " pdb=" CG MET R 281 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.02e+00 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 108.54 5.36 1.80e+00 3.09e-01 8.86e+00 angle pdb=" C LYS A 192 " pdb=" N ASP A 193 " pdb=" CA ASP A 193 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.29e+00 ... (remaining 12299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4623 17.55 - 35.10: 622 35.10 - 52.66: 170 52.66 - 70.21: 16 70.21 - 87.76: 11 Dihedral angle restraints: 5442 sinusoidal: 2153 harmonic: 3289 Sorted by residual: dihedral pdb=" CA GLU R 196 " pdb=" C GLU R 196 " pdb=" N ARG R 197 " pdb=" CA ARG R 197 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" SG CYS R 124 " pdb=" CB CYS R 203 " pdb=" SG CYS R 203 " pdb=" CA CYS R 203 " ideal model delta sinusoidal sigma weight residual -73.00 -3.44 -69.56 1 2.00e+01 2.50e-03 1.56e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1020 0.039 - 0.078: 272 0.078 - 0.118: 96 0.118 - 0.157: 18 0.157 - 0.196: 3 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA LEU R 198 " pdb=" N LEU R 198 " pdb=" C LEU R 198 " pdb=" CB LEU R 198 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA LEU R 180 " pdb=" N LEU R 180 " pdb=" C LEU R 180 " pdb=" CB LEU R 180 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 1406 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 314 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO R 315 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 315 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 315 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO S 236 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 106 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO R 107 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 107 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 107 " -0.027 5.00e-02 4.00e+02 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2452 2.81 - 3.33: 8068 3.33 - 3.85: 14375 3.85 - 4.38: 16517 4.38 - 4.90: 30026 Nonbonded interactions: 71438 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.283 3.040 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.291 3.040 nonbonded pdb=" OD2 ASP R 195 " pdb=" NE2 GLN R 204 " model vdw 2.293 3.120 nonbonded pdb=" OE1 GLU A 33 " pdb=" ND1 HIS A 195 " model vdw 2.302 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.311 3.120 ... (remaining 71433 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: 1.550 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.380 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 : 0.003 0.036 9084 Z= 0.148 Angle : 0.574 9.384 12310 Z= 0.307 Chirality : 0.042 0.196 1409 Planarity : 0.004 0.054 1551 Dihedral : 16.755 87.760 3311 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 25.68 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1120 helix: 2.27 (0.26), residues: 380 sheet: 0.20 (0.30), residues: 283 loop : -0.94 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.027 0.001 TYR S 235 PHE 0.026 0.001 PHE R 182 TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS R 193 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9081) covalent geometry : angle 0.57350 (12304) SS BOND : bond 0.00343 ( 3) SS BOND : angle 1.05410 ( 6) hydrogen bonds : bond 0.11870 ( 469) hydrogen bonds : angle 5.24301 ( 1335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.327 Fit side-chains REVERT: A 305 CYS cc_start: 0.7727 (p) cc_final: 0.7380 (m) REVERT: R 99 ASP cc_start: 0.7275 (t70) cc_final: 0.6941 (t70) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1072 time to fit residues: 19.4700 Evaluate side-chains 123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN R 193 HIS ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.121940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.091634 restraints weight = 13780.798| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.20 r_work: 0.2961 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9084 Z= 0.166 Angle : 0.572 8.403 12310 Z= 0.295 Chirality : 0.042 0.256 1409 Planarity : 0.004 0.051 1551 Dihedral : 4.952 52.147 1300 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.53 % Allowed : 25.36 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1120 helix: 2.30 (0.26), residues: 384 sheet: 0.09 (0.31), residues: 280 loop : -0.95 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.037 0.002 TYR S 235 PHE 0.020 0.001 PHE R 182 TRP 0.011 0.001 TRP R 109 HIS 0.007 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9081) covalent geometry : angle 0.57172 (12304) SS BOND : bond 0.00428 ( 3) SS BOND : angle 1.28511 ( 6) hydrogen bonds : bond 0.04265 ( 469) hydrogen bonds : angle 4.53153 ( 1335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.324 Fit side-chains outliers start: 34 outliers final: 18 residues processed: 153 average time/residue: 0.1131 time to fit residues: 23.1554 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 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 = 0.3636 r_free = 0.3636 target = 0.123647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091636 restraints weight = 13594.340| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.18 r_work: 0.2967 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9084 Z= 0.118 Angle : 0.531 8.814 12310 Z= 0.272 Chirality : 0.041 0.222 1409 Planarity : 0.004 0.048 1551 Dihedral : 4.436 49.617 1300 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.95 % Allowed : 25.57 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.26), residues: 1120 helix: 2.42 (0.27), residues: 385 sheet: 0.26 (0.31), residues: 278 loop : -0.93 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 292 TYR 0.027 0.001 TYR S 235 PHE 0.015 0.001 PHE R 207 TRP 0.008 0.001 TRP R 109 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9081) covalent geometry : angle 0.53085 (12304) SS BOND : bond 0.00352 ( 3) SS BOND : angle 1.21320 ( 6) hydrogen bonds : bond 0.03780 ( 469) hydrogen bonds : angle 4.37012 ( 1335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.361 Fit side-chains REVERT: B 96 ARG cc_start: 0.8528 (mtm110) cc_final: 0.7979 (mtt-85) REVERT: R 99 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7027 (t70) REVERT: R 190 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8066 (tp) REVERT: S 235 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.7436 (t80) outliers start: 38 outliers final: 22 residues processed: 163 average time/residue: 0.1092 time to fit residues: 23.9908 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092082 restraints weight = 13718.609| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.15 r_work: 0.2982 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9084 Z= 0.119 Angle : 0.532 8.292 12310 Z= 0.272 Chirality : 0.041 0.222 1409 Planarity : 0.004 0.050 1551 Dihedral : 4.360 49.250 1300 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.85 % Allowed : 26.09 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1120 helix: 2.43 (0.27), residues: 385 sheet: 0.31 (0.31), residues: 278 loop : -0.93 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 8 TYR 0.029 0.001 TYR S 235 PHE 0.017 0.001 PHE R 182 TRP 0.010 0.001 TRP R 117 HIS 0.006 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9081) covalent geometry : angle 0.53170 (12304) SS BOND : bond 0.00430 ( 3) SS BOND : angle 1.26972 ( 6) hydrogen bonds : bond 0.03681 ( 469) hydrogen bonds : angle 4.33042 ( 1335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.396 Fit side-chains REVERT: A 312 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8433 (mttp) REVERT: B 96 ARG cc_start: 0.8496 (mtm110) cc_final: 0.7982 (mtt-85) REVERT: R 64 PHE cc_start: 0.8275 (t80) cc_final: 0.8027 (t80) REVERT: R 68 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8418 (mm) REVERT: R 99 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7016 (t70) REVERT: S 235 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7404 (t80) outliers start: 37 outliers final: 25 residues processed: 159 average time/residue: 0.1042 time to fit residues: 22.7614 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089731 restraints weight = 13701.473| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.18 r_work: 0.2936 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9084 Z= 0.211 Angle : 0.597 9.574 12310 Z= 0.306 Chirality : 0.043 0.290 1409 Planarity : 0.004 0.055 1551 Dihedral : 4.707 52.174 1300 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.85 % Allowed : 26.40 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.26), residues: 1120 helix: 2.29 (0.26), residues: 385 sheet: 0.18 (0.31), residues: 278 loop : -0.98 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.041 0.002 TYR S 235 PHE 0.018 0.002 PHE B 253 TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9081) covalent geometry : angle 0.59675 (12304) SS BOND : bond 0.00554 ( 3) SS BOND : angle 1.48138 ( 6) hydrogen bonds : bond 0.04431 ( 469) hydrogen bonds : angle 4.52426 ( 1335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.367 Fit side-chains REVERT: B 96 ARG cc_start: 0.8499 (mtm110) cc_final: 0.7959 (mtt-85) REVERT: R 64 PHE cc_start: 0.8291 (t80) cc_final: 0.8051 (t80) REVERT: R 68 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8367 (mm) REVERT: R 99 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7033 (t70) REVERT: S 218 ARG cc_start: 0.8085 (ptp-110) cc_final: 0.7838 (ptp90) REVERT: S 235 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7727 (t80) outliers start: 37 outliers final: 27 residues processed: 160 average time/residue: 0.1134 time to fit residues: 24.3792 Evaluate side-chains 157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090811 restraints weight = 13608.352| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.12 r_work: 0.2967 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9084 Z= 0.121 Angle : 0.538 8.976 12310 Z= 0.275 Chirality : 0.041 0.219 1409 Planarity : 0.003 0.048 1551 Dihedral : 4.418 48.663 1300 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.26 % Allowed : 26.30 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.26), residues: 1120 helix: 2.45 (0.26), residues: 383 sheet: 0.19 (0.31), residues: 281 loop : -0.93 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.029 0.001 TYR S 235 PHE 0.017 0.001 PHE R 182 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9081) covalent geometry : angle 0.53789 (12304) SS BOND : bond 0.00391 ( 3) SS BOND : angle 1.17729 ( 6) hydrogen bonds : bond 0.03773 ( 469) hydrogen bonds : angle 4.37440 ( 1335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.373 Fit side-chains REVERT: B 96 ARG cc_start: 0.8476 (mtm110) cc_final: 0.7980 (mtt-85) REVERT: R 64 PHE cc_start: 0.8211 (t80) cc_final: 0.7949 (t80) REVERT: R 68 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8313 (mm) REVERT: R 99 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7013 (t70) REVERT: R 190 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8070 (tp) REVERT: S 235 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.7322 (t80) outliers start: 41 outliers final: 25 residues processed: 158 average time/residue: 0.0905 time to fit residues: 19.5145 Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090541 restraints weight = 13746.471| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.19 r_work: 0.2948 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9084 Z= 0.158 Angle : 0.565 9.115 12310 Z= 0.290 Chirality : 0.042 0.252 1409 Planarity : 0.004 0.054 1551 Dihedral : 4.498 49.777 1300 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.74 % Allowed : 26.40 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.26), residues: 1120 helix: 2.33 (0.26), residues: 385 sheet: 0.18 (0.31), residues: 278 loop : -0.97 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.036 0.002 TYR S 235 PHE 0.016 0.001 PHE R 207 TRP 0.009 0.001 TRP R 109 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9081) covalent geometry : angle 0.56492 (12304) SS BOND : bond 0.00448 ( 3) SS BOND : angle 1.26951 ( 6) hydrogen bonds : bond 0.04018 ( 469) hydrogen bonds : angle 4.43514 ( 1335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.245 Fit side-chains REVERT: R 64 PHE cc_start: 0.8238 (t80) cc_final: 0.7951 (t80) REVERT: R 68 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8316 (mm) REVERT: R 99 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7071 (t70) REVERT: S 235 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7538 (t80) outliers start: 36 outliers final: 30 residues processed: 161 average time/residue: 0.1070 time to fit residues: 23.0606 Evaluate side-chains 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.0010 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093659 restraints weight = 13639.905| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.11 r_work: 0.3011 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9084 Z= 0.103 Angle : 0.526 9.299 12310 Z= 0.269 Chirality : 0.040 0.182 1409 Planarity : 0.003 0.046 1551 Dihedral : 4.205 46.126 1300 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.22 % Allowed : 26.92 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1120 helix: 2.43 (0.27), residues: 385 sheet: 0.29 (0.31), residues: 279 loop : -0.90 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.023 0.001 TYR S 235 PHE 0.017 0.001 PHE R 182 TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9081) covalent geometry : angle 0.52559 (12304) SS BOND : bond 0.00294 ( 3) SS BOND : angle 1.04601 ( 6) hydrogen bonds : bond 0.03428 ( 469) hydrogen bonds : angle 4.26126 ( 1335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.216 Fit side-chains REVERT: A 248 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8098 (mppt) REVERT: A 289 GLU cc_start: 0.7208 (pm20) cc_final: 0.6430 (pt0) REVERT: B 96 ARG cc_start: 0.8353 (mtm110) cc_final: 0.7991 (mtt-85) REVERT: R 64 PHE cc_start: 0.8140 (t80) cc_final: 0.7843 (t80) REVERT: R 68 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8334 (mm) REVERT: R 99 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7010 (t70) outliers start: 31 outliers final: 22 residues processed: 157 average time/residue: 0.1071 time to fit residues: 22.7462 Evaluate side-chains 157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 156 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091959 restraints weight = 13651.292| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.18 r_work: 0.2974 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9084 Z= 0.123 Angle : 0.546 8.865 12310 Z= 0.279 Chirality : 0.041 0.182 1409 Planarity : 0.003 0.055 1551 Dihedral : 4.261 47.482 1300 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.01 % Allowed : 27.13 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.26), residues: 1120 helix: 2.44 (0.27), residues: 385 sheet: 0.32 (0.31), residues: 279 loop : -0.86 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.023 0.001 TYR S 235 PHE 0.022 0.001 PHE R 182 TRP 0.010 0.001 TRP R 109 HIS 0.009 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9081) covalent geometry : angle 0.54564 (12304) SS BOND : bond 0.00472 ( 3) SS BOND : angle 1.21273 ( 6) hydrogen bonds : bond 0.03622 ( 469) hydrogen bonds : angle 4.29987 ( 1335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.383 Fit side-chains REVERT: A 248 LYS cc_start: 0.8367 (mmtm) cc_final: 0.8067 (mppt) REVERT: A 289 GLU cc_start: 0.7355 (pm20) cc_final: 0.6600 (pt0) REVERT: B 96 ARG cc_start: 0.8403 (mtm110) cc_final: 0.7985 (mtt-85) REVERT: R 64 PHE cc_start: 0.8188 (t80) cc_final: 0.7902 (t80) REVERT: R 68 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8344 (mm) REVERT: R 99 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6947 (t70) REVERT: S 235 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.7180 (t80) outliers start: 29 outliers final: 23 residues processed: 148 average time/residue: 0.1066 time to fit residues: 21.4328 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 103 optimal weight: 0.0170 chunk 70 optimal weight: 0.0470 chunk 86 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.093419 restraints weight = 13557.297| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.08 r_work: 0.3003 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9084 Z= 0.107 Angle : 0.536 9.319 12310 Z= 0.273 Chirality : 0.040 0.159 1409 Planarity : 0.003 0.049 1551 Dihedral : 4.143 46.397 1300 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.01 % Allowed : 27.23 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1120 helix: 2.45 (0.27), residues: 386 sheet: 0.31 (0.31), residues: 279 loop : -0.85 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.023 0.001 TYR S 235 PHE 0.022 0.001 PHE R 182 TRP 0.009 0.001 TRP R 109 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9081) covalent geometry : angle 0.53583 (12304) SS BOND : bond 0.00421 ( 3) SS BOND : angle 1.05268 ( 6) hydrogen bonds : bond 0.03401 ( 469) hydrogen bonds : angle 4.22486 ( 1335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.251 Fit side-chains REVERT: A 248 LYS cc_start: 0.8372 (mmtm) cc_final: 0.8106 (mppt) REVERT: A 289 GLU cc_start: 0.7241 (pm20) cc_final: 0.6525 (pt0) REVERT: B 96 ARG cc_start: 0.8331 (mtm110) cc_final: 0.7985 (mtt-85) REVERT: R 64 PHE cc_start: 0.8176 (t80) cc_final: 0.7873 (t80) REVERT: R 68 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8389 (mm) REVERT: R 99 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7038 (t70) REVERT: R 266 LEU cc_start: 0.8560 (tt) cc_final: 0.7693 (mt) REVERT: S 235 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6894 (t80) outliers start: 29 outliers final: 24 residues processed: 149 average time/residue: 0.1032 time to fit residues: 21.0171 Evaluate side-chains 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.0470 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 106 optimal weight: 0.1980 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091544 restraints weight = 13490.297| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.09 r_work: 0.2973 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9084 Z= 0.136 Angle : 0.555 8.855 12310 Z= 0.284 Chirality : 0.041 0.181 1409 Planarity : 0.004 0.056 1551 Dihedral : 4.267 47.785 1300 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.91 % Allowed : 27.34 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.26), residues: 1120 helix: 2.40 (0.27), residues: 386 sheet: 0.31 (0.31), residues: 279 loop : -0.88 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.025 0.001 TYR S 235 PHE 0.030 0.001 PHE R 182 TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9081) covalent geometry : angle 0.55450 (12304) SS BOND : bond 0.00448 ( 3) SS BOND : angle 1.12977 ( 6) hydrogen bonds : bond 0.03695 ( 469) hydrogen bonds : angle 4.30331 ( 1335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.79 seconds wall clock time: 45 minutes 13.71 seconds (2713.71 seconds total)