Starting phenix.real_space_refine on Tue Feb 11 18:31:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mqy_48544/02_2025/9mqy_48544.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mqy_48544/02_2025/9mqy_48544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mqy_48544/02_2025/9mqy_48544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mqy_48544/02_2025/9mqy_48544.map" model { file = "/net/cci-nas-00/data/ceres_data/9mqy_48544/02_2025/9mqy_48544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mqy_48544/02_2025/9mqy_48544.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 16 5.16 5 C 4101 2.51 5 N 1153 2.21 5 O 1174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6448 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3153 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 19, 'TRANS': 427} Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 6, 'ASP:plan': 9, 'GLU:plan': 19, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "B" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3189 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 19, 'TRANS': 427} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'ASP:plan': 7, 'GLU:plan': 18, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 119 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.21, per 1000 atoms: 0.81 Number of scatterers: 6448 At special positions: 0 Unit cell: (109.44, 81.92, 69.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 4 15.00 O 1174 8.00 N 1153 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 972.5 milliseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 44.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.578A pdb=" N VAL A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 137 through 156 removed outlier: 3.587A pdb=" N PHE A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 176 through 192 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 236 removed outlier: 4.378A pdb=" N LEU A 225 " --> pdb=" O MET A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 4.079A pdb=" N ASP A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 329 through 349 Processing helix chain 'A' and resid 386 through 401 removed outlier: 3.751A pdb=" N TYR A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 401 " --> pdb=" O HIS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 429 through 447 removed outlier: 5.710A pdb=" N ARG A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N THR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.572A pdb=" N VAL B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.001A pdb=" N ILE B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 125 through 131 Processing helix chain 'B' and resid 137 through 156 removed outlier: 3.648A pdb=" N PHE B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 222 through 236 Processing helix chain 'B' and resid 281 through 291 removed outlier: 4.060A pdb=" N ASP B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 321 Processing helix chain 'B' and resid 329 through 349 Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.870A pdb=" N TYR B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 401 " --> pdb=" O HIS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 429 through 447 removed outlier: 5.808A pdb=" N ARG B 436 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 83 removed outlier: 8.288A pdb=" N GLN A 80 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 37 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU A 82 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU A 39 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS A 12 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LYS A 38 " --> pdb=" O HIS A 12 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 14 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE A 40 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 16 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 308 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 90 removed outlier: 5.435A pdb=" N VAL A 86 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 99 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 242 removed outlier: 6.818A pdb=" N VAL A 208 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLN A 241 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU A 210 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 250 removed outlier: 6.573A pdb=" N THR A 255 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL A 249 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 371 removed outlier: 6.690A pdb=" N SER A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 83 removed outlier: 6.677A pdb=" N VAL B 37 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 82 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 39 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 308 " --> pdb=" O HIS B 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 90 removed outlier: 5.416A pdb=" N VAL B 86 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 99 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 242 removed outlier: 6.870A pdb=" N VAL B 208 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLN B 241 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU B 210 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 245 through 250 removed outlier: 6.523A pdb=" N THR B 255 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 249 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 366 through 371 removed outlier: 6.719A pdb=" N SER B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 375 " --> pdb=" O GLY B 386 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 909 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: 2.00 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2145 1.34 - 1.45: 795 1.45 - 1.57: 3604 1.57 - 1.68: 4 1.68 - 1.80: 28 Bond restraints: 6576 Sorted by residual: bond pdb=" O5B FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sigma weight residual 1.634 1.539 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.568 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O3P FAD B 501 " pdb=" P FAD B 501 " ideal model delta sigma weight residual 1.660 1.575 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" O5B FAD B 501 " pdb=" PA FAD B 501 " ideal model delta sigma weight residual 1.634 1.561 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" O5' FAD B 501 " pdb=" P FAD B 501 " ideal model delta sigma weight residual 1.637 1.567 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 6571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 8731 1.82 - 3.63: 241 3.63 - 5.45: 22 5.45 - 7.26: 6 7.26 - 9.08: 2 Bond angle restraints: 9002 Sorted by residual: angle pdb=" N GLN A 49 " pdb=" CA GLN A 49 " pdb=" C GLN A 49 " ideal model delta sigma weight residual 109.81 116.55 -6.74 2.21e+00 2.05e-01 9.30e+00 angle pdb=" O1P FAD A 501 " pdb=" P FAD A 501 " pdb=" O2P FAD A 501 " ideal model delta sigma weight residual 122.50 113.42 9.08 3.00e+00 1.11e-01 9.16e+00 angle pdb=" C ASN A 252 " pdb=" N GLY A 253 " pdb=" CA GLY A 253 " ideal model delta sigma weight residual 120.72 116.96 3.76 1.33e+00 5.65e-01 8.01e+00 angle pdb=" O1A FAD B 501 " pdb=" PA FAD B 501 " pdb=" O5B FAD B 501 " ideal model delta sigma weight residual 104.10 112.44 -8.34 3.00e+00 1.11e-01 7.73e+00 angle pdb=" C ASN B 252 " pdb=" N GLY B 253 " pdb=" CA GLY B 253 " ideal model delta sigma weight residual 120.91 117.11 3.80 1.38e+00 5.25e-01 7.56e+00 ... (remaining 8997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 3767 22.41 - 44.81: 91 44.81 - 67.22: 22 67.22 - 89.63: 9 89.63 - 112.04: 1 Dihedral angle restraints: 3890 sinusoidal: 1370 harmonic: 2520 Sorted by residual: dihedral pdb=" CA ARG B 296 " pdb=" C ARG B 296 " pdb=" N ALA B 297 " pdb=" CA ALA B 297 " ideal model delta harmonic sigma weight residual 180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE A 201 " pdb=" C ILE A 201 " pdb=" N ASP A 202 " pdb=" CA ASP A 202 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ASP B 295 " pdb=" C ASP B 295 " pdb=" N ARG B 296 " pdb=" CA ARG B 296 " ideal model delta harmonic sigma weight residual 180.00 159.02 20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 3887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 570 0.034 - 0.069: 348 0.069 - 0.103: 116 0.103 - 0.137: 51 0.137 - 0.171: 9 Chirality restraints: 1094 Sorted by residual: chirality pdb=" CA ILE B 254 " pdb=" N ILE B 254 " pdb=" C ILE B 254 " pdb=" CB ILE B 254 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" C2B FAD B 501 " pdb=" C1B FAD B 501 " pdb=" C3B FAD B 501 " pdb=" O2B FAD B 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.71 0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA PRO B 50 " pdb=" N PRO B 50 " pdb=" C PRO B 50 " pdb=" CB PRO B 50 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 1091 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 283 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLY B 283 " -0.060 2.00e-02 2.50e+03 pdb=" O GLY B 283 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS B 284 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 147 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C ARG A 147 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG A 147 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 148 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 283 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLY A 283 " 0.058 2.00e-02 2.50e+03 pdb=" O GLY A 283 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS A 284 " -0.019 2.00e-02 2.50e+03 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2494 2.88 - 3.39: 6197 3.39 - 3.89: 10917 3.89 - 4.40: 12627 4.40 - 4.90: 21665 Nonbonded interactions: 53900 Sorted by model distance: nonbonded pdb=" OD1 ASP A 305 " pdb=" OG1 THR A 307 " model vdw 2.375 3.040 nonbonded pdb=" OD1 ASP B 305 " pdb=" OG1 THR B 307 " model vdw 2.403 3.040 nonbonded pdb=" NH2 ARG B 11 " pdb=" OD1 ASP B 34 " model vdw 2.412 3.120 nonbonded pdb=" O PHE B 21 " pdb=" OG1 THR B 25 " model vdw 2.444 3.040 nonbonded pdb=" OH TYR B 339 " pdb=" O THR B 357 " model vdw 2.455 3.040 ... (remaining 53895 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 2 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 31 or (resid 32 through 33 and (nam \ e N or name CA or name C or name O or name CB )) or resid 34 through 37 or (resi \ d 38 and (name N or name CA or name C or name O or name CB )) or resid 39 throug \ h 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or re \ sid 65 through 190 or (resid 191 and (name N or name CA or name C or name O or n \ ame CB )) or resid 192 through 250 or (resid 251 and (name N or name CA or name \ C or name O or name CB )) or resid 252 through 257 or (resid 258 and (name N or \ name CA or name C or name O or name CB )) or resid 259 through 437 or (resid 438 \ and (name N or name CA or name C or name O or name CB )) or resid 439 through 4 \ 48 or resid 501)) } 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: 9.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.430 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.007 0.095 6576 Z= 0.460 Angle : 0.749 9.079 9002 Z= 0.426 Chirality : 0.051 0.171 1094 Planarity : 0.009 0.098 1138 Dihedral : 12.524 112.035 2278 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.67 % Allowed : 3.83 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 890 helix: -0.80 (0.24), residues: 340 sheet: 0.27 (0.38), residues: 182 loop : -1.13 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.009 TRP A 393 HIS 0.006 0.002 HIS A 127 PHE 0.017 0.003 PHE A 384 TYR 0.024 0.005 TYR B 53 ARG 0.020 0.003 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.672 Fit side-chains REVERT: B 153 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8726 (mm-30) REVERT: B 438 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7521 (ttm170) outliers start: 4 outliers final: 1 residues processed: 79 average time/residue: 1.2757 time to fit residues: 106.0151 Evaluate side-chains 51 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 93 ASN B 93 ASN B 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.070025 restraints weight = 11308.106| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.46 r_work: 0.2618 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6576 Z= 0.270 Angle : 0.532 5.984 9002 Z= 0.283 Chirality : 0.046 0.153 1094 Planarity : 0.004 0.038 1138 Dihedral : 8.519 103.569 1048 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.17 % Allowed : 7.50 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 890 helix: 1.00 (0.27), residues: 346 sheet: 0.25 (0.38), residues: 172 loop : -0.38 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 390 HIS 0.003 0.001 HIS B 12 PHE 0.010 0.001 PHE B 384 TYR 0.011 0.001 TYR B 109 ARG 0.004 0.001 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.756 Fit side-chains REVERT: A 250 ASP cc_start: 0.8602 (m-30) cc_final: 0.8261 (m-30) REVERT: A 405 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8661 (tmtp) REVERT: B 64 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: B 78 ASN cc_start: 0.8840 (m-40) cc_final: 0.8568 (t0) REVERT: B 153 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8943 (mm-30) REVERT: B 156 GLU cc_start: 0.9269 (mm-30) cc_final: 0.9048 (mm-30) REVERT: B 438 ARG cc_start: 0.8246 (mmm160) cc_final: 0.7663 (ttm170) outliers start: 13 outliers final: 6 residues processed: 63 average time/residue: 1.1887 time to fit residues: 79.2553 Evaluate side-chains 53 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.0050 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.082748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.068473 restraints weight = 11246.051| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.56 r_work: 0.2622 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6576 Z= 0.188 Angle : 0.459 5.521 9002 Z= 0.243 Chirality : 0.044 0.144 1094 Planarity : 0.004 0.041 1138 Dihedral : 8.003 95.616 1047 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.33 % Allowed : 8.33 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.28), residues: 890 helix: 1.55 (0.28), residues: 350 sheet: 0.18 (0.42), residues: 148 loop : -0.26 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 390 HIS 0.002 0.001 HIS A 397 PHE 0.008 0.001 PHE A 384 TYR 0.008 0.001 TYR B 109 ARG 0.002 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.683 Fit side-chains REVERT: A 250 ASP cc_start: 0.8580 (m-30) cc_final: 0.8275 (m-30) REVERT: B 24 LEU cc_start: 0.8442 (tp) cc_final: 0.8237 (tm) REVERT: B 64 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: B 78 ASN cc_start: 0.8843 (m-40) cc_final: 0.8588 (t0) REVERT: B 153 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8901 (mm-30) REVERT: B 156 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8949 (mm-30) REVERT: B 250 ASP cc_start: 0.8488 (m-30) cc_final: 0.8238 (m-30) REVERT: B 438 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7731 (ttm170) outliers start: 14 outliers final: 4 residues processed: 61 average time/residue: 1.1192 time to fit residues: 72.6950 Evaluate side-chains 50 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.082054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.067869 restraints weight = 11337.078| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.55 r_work: 0.2611 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6576 Z= 0.227 Angle : 0.459 5.729 9002 Z= 0.239 Chirality : 0.044 0.149 1094 Planarity : 0.004 0.043 1138 Dihedral : 7.532 87.717 1047 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.17 % Allowed : 9.33 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 890 helix: 1.70 (0.28), residues: 350 sheet: -0.13 (0.39), residues: 158 loop : -0.19 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 390 HIS 0.003 0.001 HIS A 397 PHE 0.007 0.001 PHE A 152 TYR 0.007 0.001 TYR B 109 ARG 0.003 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.747 Fit side-chains REVERT: A 250 ASP cc_start: 0.8597 (m-30) cc_final: 0.8308 (m-30) REVERT: B 78 ASN cc_start: 0.8889 (m-40) cc_final: 0.8645 (t0) REVERT: B 156 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8928 (mm-30) REVERT: B 250 ASP cc_start: 0.8541 (m-30) cc_final: 0.8300 (m-30) REVERT: B 438 ARG cc_start: 0.8276 (mmm160) cc_final: 0.7735 (ttm170) outliers start: 13 outliers final: 4 residues processed: 56 average time/residue: 1.2064 time to fit residues: 71.6986 Evaluate side-chains 48 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.067927 restraints weight = 11194.312| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.53 r_work: 0.2610 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6576 Z= 0.216 Angle : 0.449 5.787 9002 Z= 0.233 Chirality : 0.044 0.159 1094 Planarity : 0.004 0.044 1138 Dihedral : 7.061 85.168 1047 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.33 % Allowed : 10.33 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.29), residues: 890 helix: 1.84 (0.28), residues: 350 sheet: -0.23 (0.37), residues: 182 loop : -0.07 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 390 HIS 0.003 0.001 HIS A 397 PHE 0.007 0.001 PHE A 152 TYR 0.007 0.001 TYR B 109 ARG 0.002 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.726 Fit side-chains REVERT: A 250 ASP cc_start: 0.8626 (m-30) cc_final: 0.8356 (m-30) REVERT: A 405 LYS cc_start: 0.8907 (tmmt) cc_final: 0.8670 (tmtm) REVERT: B 78 ASN cc_start: 0.8927 (m-40) cc_final: 0.8710 (t0) REVERT: B 156 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8934 (mm-30) REVERT: B 250 ASP cc_start: 0.8587 (m-30) cc_final: 0.8356 (m-30) REVERT: B 438 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7766 (ttm170) outliers start: 14 outliers final: 7 residues processed: 69 average time/residue: 1.2552 time to fit residues: 91.2643 Evaluate side-chains 53 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.080765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.066510 restraints weight = 11214.646| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.52 r_work: 0.2586 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6576 Z= 0.321 Angle : 0.484 5.908 9002 Z= 0.250 Chirality : 0.045 0.161 1094 Planarity : 0.004 0.042 1138 Dihedral : 6.927 89.749 1047 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.33 % Allowed : 11.00 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.28), residues: 890 helix: 1.84 (0.28), residues: 350 sheet: -0.42 (0.36), residues: 182 loop : -0.10 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 390 HIS 0.002 0.001 HIS B 12 PHE 0.008 0.001 PHE A 152 TYR 0.008 0.001 TYR B 109 ARG 0.002 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.782 Fit side-chains REVERT: A 250 ASP cc_start: 0.8673 (m-30) cc_final: 0.8410 (m-30) REVERT: B 78 ASN cc_start: 0.9007 (m-40) cc_final: 0.8775 (t0) REVERT: B 248 ASP cc_start: 0.8895 (t0) cc_final: 0.8406 (t0) REVERT: B 250 ASP cc_start: 0.8619 (m-30) cc_final: 0.8024 (m-30) REVERT: B 438 ARG cc_start: 0.8287 (mmm160) cc_final: 0.7774 (ttm170) outliers start: 14 outliers final: 9 residues processed: 62 average time/residue: 1.1051 time to fit residues: 72.9510 Evaluate side-chains 54 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 366 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 311 HIS B 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.082402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.068251 restraints weight = 11150.519| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.51 r_work: 0.2617 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6576 Z= 0.163 Angle : 0.439 5.834 9002 Z= 0.227 Chirality : 0.043 0.158 1094 Planarity : 0.004 0.044 1138 Dihedral : 6.736 87.360 1047 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.33 % Allowed : 11.67 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 890 helix: 2.02 (0.28), residues: 350 sheet: -0.36 (0.36), residues: 182 loop : -0.07 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 393 HIS 0.003 0.000 HIS A 397 PHE 0.006 0.001 PHE A 152 TYR 0.006 0.001 TYR A 109 ARG 0.001 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.757 Fit side-chains REVERT: A 250 ASP cc_start: 0.8675 (m-30) cc_final: 0.8402 (m-30) REVERT: B 78 ASN cc_start: 0.8943 (m-40) cc_final: 0.8702 (t0) REVERT: B 156 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8942 (mm-30) REVERT: B 248 ASP cc_start: 0.8905 (t0) cc_final: 0.8451 (t0) REVERT: B 250 ASP cc_start: 0.8603 (m-30) cc_final: 0.8019 (m-30) REVERT: B 405 LYS cc_start: 0.8954 (tmmt) cc_final: 0.8737 (tmtm) REVERT: B 438 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7781 (ttm170) outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 1.1241 time to fit residues: 79.9958 Evaluate side-chains 61 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.083111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.068907 restraints weight = 11231.092| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.51 r_work: 0.2623 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6576 Z= 0.167 Angle : 0.438 5.877 9002 Z= 0.226 Chirality : 0.043 0.156 1094 Planarity : 0.004 0.043 1138 Dihedral : 6.586 80.542 1047 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.67 % Allowed : 12.17 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 890 helix: 2.12 (0.28), residues: 350 sheet: -0.33 (0.36), residues: 182 loop : -0.05 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 390 HIS 0.003 0.001 HIS A 397 PHE 0.007 0.001 PHE A 152 TYR 0.006 0.001 TYR B 109 ARG 0.002 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.694 Fit side-chains REVERT: A 250 ASP cc_start: 0.8656 (m-30) cc_final: 0.8400 (m-30) REVERT: B 78 ASN cc_start: 0.8943 (m-40) cc_final: 0.8737 (t0) REVERT: B 156 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8981 (mm-30) REVERT: B 248 ASP cc_start: 0.8897 (t0) cc_final: 0.8447 (t0) REVERT: B 250 ASP cc_start: 0.8595 (m-30) cc_final: 0.8009 (m-30) REVERT: B 405 LYS cc_start: 0.8935 (tmmt) cc_final: 0.8728 (tmtm) REVERT: B 438 ARG cc_start: 0.8302 (mmm160) cc_final: 0.7674 (ttm170) outliers start: 16 outliers final: 12 residues processed: 69 average time/residue: 1.0806 time to fit residues: 80.1632 Evaluate side-chains 65 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 57 optimal weight: 0.0010 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.083139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.068799 restraints weight = 11236.249| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.53 r_work: 0.2625 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6576 Z= 0.167 Angle : 0.457 10.897 9002 Z= 0.229 Chirality : 0.043 0.152 1094 Planarity : 0.004 0.043 1138 Dihedral : 6.386 72.331 1047 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.50 % Allowed : 12.83 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.29), residues: 890 helix: 2.07 (0.28), residues: 352 sheet: -0.29 (0.37), residues: 182 loop : -0.05 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 390 HIS 0.003 0.000 HIS A 397 PHE 0.006 0.001 PHE A 152 TYR 0.006 0.001 TYR B 109 ARG 0.003 0.000 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.756 Fit side-chains REVERT: A 250 ASP cc_start: 0.8648 (m-30) cc_final: 0.8397 (m-30) REVERT: B 78 ASN cc_start: 0.8933 (m-40) cc_final: 0.8729 (t0) REVERT: B 156 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8986 (mm-30) REVERT: B 250 ASP cc_start: 0.8588 (m-30) cc_final: 0.8373 (m-30) REVERT: B 438 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7764 (ttm170) outliers start: 15 outliers final: 10 residues processed: 65 average time/residue: 1.0848 time to fit residues: 75.0970 Evaluate side-chains 58 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.080770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.067127 restraints weight = 11589.187| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.44 r_work: 0.2569 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6576 Z= 0.439 Angle : 0.555 10.335 9002 Z= 0.282 Chirality : 0.047 0.161 1094 Planarity : 0.004 0.041 1138 Dihedral : 6.556 58.743 1047 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.50 % Allowed : 12.67 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.28), residues: 890 helix: 1.90 (0.28), residues: 350 sheet: -0.53 (0.36), residues: 182 loop : -0.13 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 390 HIS 0.003 0.001 HIS B 12 PHE 0.009 0.001 PHE A 152 TYR 0.009 0.001 TYR A 109 ARG 0.003 0.000 ARG B 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.766 Fit side-chains REVERT: B 78 ASN cc_start: 0.9074 (m-40) cc_final: 0.8854 (t0) REVERT: B 156 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9150 (mm-30) REVERT: B 438 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7805 (ttm170) outliers start: 15 outliers final: 11 residues processed: 60 average time/residue: 1.2307 time to fit residues: 78.2559 Evaluate side-chains 55 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.0170 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.082279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.067912 restraints weight = 11370.580| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.55 r_work: 0.2611 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6576 Z= 0.181 Angle : 0.480 10.413 9002 Z= 0.242 Chirality : 0.044 0.159 1094 Planarity : 0.004 0.042 1138 Dihedral : 5.015 48.690 1047 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.00 % Allowed : 13.33 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 890 helix: 2.01 (0.28), residues: 350 sheet: -0.39 (0.37), residues: 182 loop : -0.07 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 390 HIS 0.003 0.000 HIS A 397 PHE 0.007 0.001 PHE A 152 TYR 0.007 0.001 TYR A 109 ARG 0.002 0.000 ARG B 438 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4028.99 seconds wall clock time: 72 minutes 10.09 seconds (4330.09 seconds total)