Starting phenix.real_space_refine on Tue Mar 11 17:57:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mqy_48544/03_2025/9mqy_48544.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mqy_48544/03_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_48544/03_2025/9mqy_48544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mqy_48544/03_2025/9mqy_48544.map" model { file = "/net/cci-nas-00/data/ceres_data/9mqy_48544/03_2025/9mqy_48544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mqy_48544/03_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-5624/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: 5.19, per 1000 atoms: 0.80 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 982.8 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: 0.88 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: 1.95 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: 2.270 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.130 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- 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 : 0.610 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: 1.2457 time to fit residues: 103.5464 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 : 0.724 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.070013 restraints weight = 11308.093| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.46 r_work: 0.2615 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- 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 : 0.674 Fit side-chains REVERT: A 250 ASP cc_start: 0.8603 (m-30) cc_final: 0.8262 (m-30) REVERT: A 405 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8664 (tmtp) REVERT: B 64 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: B 78 ASN cc_start: 0.8841 (m-40) cc_final: 0.8569 (t0) REVERT: B 153 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8944 (mm-30) REVERT: B 156 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9048 (mm-30) REVERT: B 438 ARG cc_start: 0.8247 (mmm160) cc_final: 0.7665 (ttm170) outliers start: 13 outliers final: 6 residues processed: 63 average time/residue: 1.1467 time to fit residues: 76.8393 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 : 0.719 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.080478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.066593 restraints weight = 11381.521| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.47 r_work: 0.2589 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1579 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= 0.334 Angle : 0.510 5.689 9002 Z= 0.267 Chirality : 0.046 0.168 1094 Planarity : 0.004 0.041 1138 Dihedral : 7.964 90.668 1047 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.67 % Allowed : 8.00 % 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: 0.58 (0.28), residues: 890 helix: 1.40 (0.27), residues: 350 sheet: 0.03 (0.40), residues: 158 loop : -0.32 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 390 HIS 0.003 0.001 HIS B 12 PHE 0.010 0.001 PHE A 152 TYR 0.009 0.001 TYR B 109 ARG 0.003 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: 16 poor density : 49 time to evaluate : 0.784 Fit side-chains REVERT: A 250 ASP cc_start: 0.8661 (m-30) cc_final: 0.8347 (m-30) REVERT: B 78 ASN cc_start: 0.8976 (m-40) cc_final: 0.8736 (t0) REVERT: B 156 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9024 (mm-30) REVERT: B 438 ARG cc_start: 0.8273 (mmm160) cc_final: 0.7728 (ttm170) outliers start: 16 outliers final: 5 residues processed: 61 average time/residue: 1.2434 time to fit residues: 80.3423 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 : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 329 VAL 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: 2.9990 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.2990 r_free = 0.2990 target = 0.081868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.067671 restraints weight = 11297.716| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.54 r_work: 0.2608 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1845 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= 0.209 Angle : 0.458 5.676 9002 Z= 0.240 Chirality : 0.044 0.153 1094 Planarity : 0.004 0.043 1138 Dihedral : 7.340 83.800 1047 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.33 % Allowed : 9.17 % 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: 0.73 (0.28), residues: 890 helix: 1.67 (0.28), residues: 350 sheet: -0.24 (0.39), residues: 158 loop : -0.22 (0.32), residues: 382 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 0.008 0.001 PHE B 152 TYR 0.007 0.001 TYR B 109 ARG 0.002 0.000 ARG B 264 *********************** 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 64 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.726 Fit side-chains REVERT: A 250 ASP cc_start: 0.8633 (m-30) cc_final: 0.8343 (m-30) REVERT: B 78 ASN cc_start: 0.8965 (m-40) cc_final: 0.8747 (t0) REVERT: B 156 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8961 (mm-30) REVERT: B 250 ASP cc_start: 0.8564 (m-30) cc_final: 0.8328 (m-30) REVERT: B 438 ARG cc_start: 0.8287 (mmm160) cc_final: 0.7743 (ttm170) outliers start: 14 outliers final: 6 residues processed: 61 average time/residue: 1.0618 time to fit residues: 69.1912 Evaluate side-chains 51 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 329 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3003 r_free = 0.3003 target = 0.083606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.069883 restraints weight = 11315.175| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.46 r_work: 0.2604 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1977 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= 0.230 Angle : 0.461 5.810 9002 Z= 0.238 Chirality : 0.044 0.155 1094 Planarity : 0.004 0.043 1138 Dihedral : 7.041 88.441 1047 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.67 % Allowed : 9.83 % Favored : 87.50 % 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: 0.87 (0.29), residues: 890 helix: 1.82 (0.28), residues: 350 sheet: -0.30 (0.37), residues: 182 loop : -0.08 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 A 109 ARG 0.002 0.000 ARG B 264 *********************** 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 73 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.662 Fit side-chains REVERT: A 250 ASP cc_start: 0.8654 (m-30) cc_final: 0.8390 (m-30) REVERT: B 78 ASN cc_start: 0.8976 (m-40) cc_final: 0.8749 (t0) REVERT: B 156 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8968 (mm-30) REVERT: B 250 ASP cc_start: 0.8595 (m-30) cc_final: 0.8372 (m-30) REVERT: B 438 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7769 (ttm170) outliers start: 16 outliers final: 10 residues processed: 71 average time/residue: 1.2165 time to fit residues: 91.2756 Evaluate side-chains 57 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 329 VAL 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 396 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 0.0470 chunk 73 optimal weight: 6.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- 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 = 0.2986 r_free = 0.2986 target = 0.082599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.068778 restraints weight = 11309.467| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.47 r_work: 0.2583 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2083 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= 0.299 Angle : 0.476 6.021 9002 Z= 0.246 Chirality : 0.044 0.158 1094 Planarity : 0.004 0.042 1138 Dihedral : 6.882 87.930 1047 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.83 % Allowed : 10.67 % Favored : 86.50 % 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: 0.83 (0.28), residues: 890 helix: 1.86 (0.28), residues: 350 sheet: -0.48 (0.36), residues: 182 loop : -0.10 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 390 HIS 0.003 0.001 HIS A 397 PHE 0.008 0.001 PHE A 152 TYR 0.008 0.001 TYR A 109 ARG 0.002 0.000 ARG A 147 *********************** 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 67 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.669 Fit side-chains REVERT: A 250 ASP cc_start: 0.8683 (m-30) cc_final: 0.8420 (m-30) REVERT: B 78 ASN cc_start: 0.9030 (m-40) cc_final: 0.8807 (t0) REVERT: B 248 ASP cc_start: 0.8903 (t0) cc_final: 0.8411 (t0) REVERT: B 250 ASP cc_start: 0.8614 (m-30) cc_final: 0.8043 (m-30) REVERT: B 438 ARG cc_start: 0.8302 (mmm160) cc_final: 0.7787 (ttm170) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 1.0011 time to fit residues: 70.6959 Evaluate side-chains 57 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 329 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.0020 chunk 27 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3023 r_free = 0.3023 target = 0.084194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.070312 restraints weight = 11184.012| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.48 r_work: 0.2629 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 0.029 6576 Z= 0.145 Angle : 0.433 5.835 9002 Z= 0.224 Chirality : 0.043 0.149 1094 Planarity : 0.004 0.043 1138 Dihedral : 6.684 84.884 1047 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.83 % Allowed : 12.17 % 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: 1.03 (0.29), residues: 890 helix: 2.08 (0.28), residues: 350 sheet: -0.36 (0.36), residues: 182 loop : -0.06 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 393 HIS 0.003 0.001 HIS A 397 PHE 0.006 0.001 PHE A 152 TYR 0.006 0.001 TYR B 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: 11 poor density : 58 time to evaluate : 0.659 Fit side-chains REVERT: A 250 ASP cc_start: 0.8663 (m-30) cc_final: 0.8405 (m-30) REVERT: B 78 ASN cc_start: 0.8951 (m-40) cc_final: 0.8733 (t0) REVERT: B 156 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8978 (mm-30) REVERT: B 248 ASP cc_start: 0.8885 (t0) cc_final: 0.8429 (t0) REVERT: B 250 ASP cc_start: 0.8606 (m-30) cc_final: 0.8018 (m-30) REVERT: B 405 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8734 (tmtm) REVERT: B 438 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7659 (ttm170) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 1.0700 time to fit residues: 76.4726 Evaluate side-chains 59 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 382 VAL Chi-restraints excluded: chain B residue 9 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 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: 0.8980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.2957 r_free = 0.2957 target = 0.080080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.065994 restraints weight = 11483.295| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.48 r_work: 0.2579 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6576 Z= 0.345 Angle : 0.513 10.734 9002 Z= 0.258 Chirality : 0.045 0.154 1094 Planarity : 0.004 0.042 1138 Dihedral : 6.763 78.000 1047 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.83 % Allowed : 12.33 % 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: 0.90 (0.28), residues: 890 helix: 1.97 (0.28), residues: 350 sheet: -0.47 (0.36), residues: 182 loop : -0.10 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.004 0.000 ARG B 438 *********************** 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 64 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.638 Fit side-chains REVERT: A 250 ASP cc_start: 0.8715 (m-30) cc_final: 0.8476 (m-30) REVERT: B 78 ASN cc_start: 0.9052 (m-40) cc_final: 0.8831 (t0) REVERT: B 120 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7196 (pp30) REVERT: B 438 ARG cc_start: 0.8336 (mmm160) cc_final: 0.7780 (ttm170) outliers start: 17 outliers final: 11 residues processed: 63 average time/residue: 1.0998 time to fit residues: 73.6434 Evaluate side-chains 58 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 120 GLN 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 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: 0.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.0050 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.2999 r_free = 0.2999 target = 0.082645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.068267 restraints weight = 11316.639| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.56 r_work: 0.2615 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2389 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= 0.152 Angle : 0.464 10.074 9002 Z= 0.234 Chirality : 0.043 0.155 1094 Planarity : 0.004 0.043 1138 Dihedral : 6.627 72.667 1047 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.33 % Allowed : 13.17 % Favored : 84.50 % 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: 1.02 (0.29), residues: 890 helix: 2.07 (0.28), residues: 350 sheet: -0.37 (0.36), residues: 182 loop : -0.06 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 393 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 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 66 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.741 Fit side-chains REVERT: A 250 ASP cc_start: 0.8674 (m-30) cc_final: 0.8409 (m-30) REVERT: B 78 ASN cc_start: 0.8983 (m-40) cc_final: 0.8755 (t0) REVERT: B 250 ASP cc_start: 0.8628 (m-30) cc_final: 0.8418 (m-30) REVERT: B 438 ARG cc_start: 0.8288 (mmm160) cc_final: 0.7780 (ttm170) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 1.0930 time to fit residues: 75.8623 Evaluate side-chains 60 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 262 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 329 VAL 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: 0.6980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- 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 = 0.2983 r_free = 0.2983 target = 0.082347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.068562 restraints weight = 11582.551| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.43 r_work: 0.2585 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6576 Z= 0.326 Angle : 0.515 10.277 9002 Z= 0.260 Chirality : 0.045 0.170 1094 Planarity : 0.004 0.042 1138 Dihedral : 6.784 60.138 1047 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.50 % Allowed : 13.33 % Favored : 84.17 % 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: 0.88 (0.29), residues: 890 helix: 1.93 (0.28), residues: 350 sheet: -0.48 (0.36), residues: 182 loop : -0.09 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 390 HIS 0.002 0.001 HIS B 12 PHE 0.008 0.001 PHE A 152 TYR 0.008 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 63 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.713 Fit side-chains REVERT: B 78 ASN cc_start: 0.9064 (m-40) cc_final: 0.8841 (t0) REVERT: B 120 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7176 (pp30) REVERT: B 438 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7794 (ttm170) outliers start: 15 outliers final: 10 residues processed: 63 average time/residue: 1.1230 time to fit residues: 75.1724 Evaluate side-chains 58 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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 120 GLN 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 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: 2.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.2952 r_free = 0.2952 target = 0.079917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.065850 restraints weight = 11625.605| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.48 r_work: 0.2575 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6576 Z= 0.349 Angle : 0.530 10.027 9002 Z= 0.267 Chirality : 0.046 0.186 1094 Planarity : 0.004 0.041 1138 Dihedral : 5.471 47.084 1047 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.17 % Allowed : 14.00 % Favored : 83.83 % 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: 0.80 (0.29), residues: 890 helix: 1.88 (0.28), residues: 350 sheet: -0.55 (0.36), residues: 182 loop : -0.13 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 390 HIS 0.002 0.001 HIS B 12 PHE 0.008 0.001 PHE B 152 TYR 0.009 0.001 TYR A 109 ARG 0.002 0.000 ARG B 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4232.20 seconds wall clock time: 72 minutes 55.61 seconds (4375.61 seconds total)