Starting phenix.real_space_refine on Tue Jul 29 16:12:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5k11_8193/07_2025/5k11_8193.cif Found real_map, /net/cci-nas-00/data/ceres_data/5k11_8193/07_2025/5k11_8193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5k11_8193/07_2025/5k11_8193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5k11_8193/07_2025/5k11_8193.map" model { file = "/net/cci-nas-00/data/ceres_data/5k11_8193/07_2025/5k11_8193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5k11_8193/07_2025/5k11_8193.cif" } resolution = 3.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6334 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 38 5.16 5 C 4016 2.51 5 N 1074 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6338 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3121 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 5.39, per 1000 atoms: 0.85 Number of scatterers: 6338 At special positions: 0 Unit cell: (103.455, 73.755, 82.17, 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 38 16.00 P 6 15.00 O 1204 8.00 N 1074 7.00 C 4016 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: 1.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 49.1% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 removed outlier: 3.526A pdb=" N GLU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.656A pdb=" N LYS A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 removed outlier: 3.591A pdb=" N PHE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 186 through 204 Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.835A pdb=" N ASP A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 removed outlier: 4.474A pdb=" N GLN A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.610A pdb=" N MET A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 329 through 348 removed outlier: 3.803A pdb=" N TRP A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 369 removed outlier: 3.786A pdb=" N PHE A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.711A pdb=" N TYR A 391 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 413 removed outlier: 3.879A pdb=" N MET A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 29 removed outlier: 3.526A pdb=" N GLU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 54 through 68 removed outlier: 3.656A pdb=" N LYS B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.590A pdb=" N PHE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 186 through 204 Processing helix chain 'B' and resid 216 through 232 removed outlier: 3.834A pdb=" N ASP B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 removed outlier: 4.473A pdb=" N GLN B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.610A pdb=" N MET B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 329 through 348 removed outlier: 3.803A pdb=" N TRP B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 369 removed outlier: 3.786A pdb=" N PHE B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 381 Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.711A pdb=" N TYR B 391 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 413 removed outlier: 3.878A pdb=" N MET B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 14 removed outlier: 4.933A pdb=" N ILE A 5 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP A 38 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY A 7 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N HIS A 40 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N SER A 9 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N TYR A 42 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N VAL A 11 " --> pdb=" O TYR A 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 72 removed outlier: 4.028A pdb=" N ALA A 307 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 129 " --> pdb=" O TRP A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 144 removed outlier: 3.554A pdb=" N THR A 142 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 142 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208 removed outlier: 6.351A pdb=" N LEU A 207 " --> pdb=" O GLU A 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 14 removed outlier: 4.933A pdb=" N ILE B 5 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP B 38 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY B 7 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N HIS B 40 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N SER B 9 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N TYR B 42 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 9.806A pdb=" N VAL B 11 " --> pdb=" O TYR B 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 72 removed outlier: 4.027A pdb=" N ALA B 307 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 129 " --> pdb=" O TRP B 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.351A pdb=" N LEU B 207 " --> pdb=" O GLU B 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 310 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 2.06 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: 1988 1.34 - 1.46: 1296 1.46 - 1.58: 3112 1.58 - 1.70: 10 1.70 - 1.82: 64 Bond restraints: 6470 Sorted by residual: bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.610 0.223 3.80e-02 6.93e+02 3.45e+01 bond pdb=" O2B NDP B 501 " pdb=" P2B NDP B 501 " ideal model delta sigma weight residual 1.833 1.611 0.222 3.80e-02 6.93e+02 3.43e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.609 0.148 3.50e-02 8.16e+02 1.79e+01 bond pdb=" O5D NDP B 501 " pdb=" PN NDP B 501 " ideal model delta sigma weight residual 1.757 1.610 0.147 3.50e-02 8.16e+02 1.77e+01 bond pdb=" C2B NDP A 501 " pdb=" O2B NDP A 501 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.90e-02 1.19e+03 1.10e+01 ... (remaining 6465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 8533 3.32 - 6.64: 173 6.64 - 9.96: 24 9.96 - 13.27: 2 13.27 - 16.59: 4 Bond angle restraints: 8736 Sorted by residual: angle pdb=" C5B NDP B 501 " pdb=" O5B NDP B 501 " pdb=" PA NDP B 501 " ideal model delta sigma weight residual 103.84 120.43 -16.59 1.91e+00 2.73e-01 7.51e+01 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 120.40 -16.56 1.91e+00 2.73e-01 7.48e+01 angle pdb=" PA NDP B 501 " pdb=" O3 NDP B 501 " pdb=" PN NDP B 501 " ideal model delta sigma weight residual 107.74 120.34 -12.60 1.95e+00 2.62e-01 4.16e+01 angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 120.31 -12.57 1.95e+00 2.62e-01 4.14e+01 angle pdb=" C5D NDP B 501 " pdb=" O5D NDP B 501 " pdb=" PN NDP B 501 " ideal model delta sigma weight residual 104.93 120.48 -15.55 2.66e+00 1.41e-01 3.42e+01 ... (remaining 8731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.22: 3786 29.22 - 58.44: 42 58.44 - 87.66: 12 87.66 - 116.88: 0 116.88 - 146.11: 2 Dihedral angle restraints: 3842 sinusoidal: 1564 harmonic: 2278 Sorted by residual: dihedral pdb=" CA PHE B 334 " pdb=" C PHE B 334 " pdb=" N ALA B 335 " pdb=" CA ALA B 335 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE A 334 " pdb=" C PHE A 334 " pdb=" N ALA A 335 " pdb=" CA ALA A 335 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ALA B 241 " pdb=" C ALA B 241 " pdb=" N GLN B 242 " pdb=" CA GLN B 242 " ideal model delta harmonic sigma weight residual -180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 3839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 595 0.050 - 0.100: 279 0.100 - 0.151: 66 0.151 - 0.201: 10 0.201 - 0.251: 4 Chirality restraints: 954 Sorted by residual: chirality pdb=" CB ILE A 244 " pdb=" CA ILE A 244 " pdb=" CG1 ILE A 244 " pdb=" CG2 ILE A 244 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE B 244 " pdb=" CA ILE B 244 " pdb=" CG1 ILE B 244 " pdb=" CG2 ILE B 244 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB VAL A 255 " pdb=" CA VAL A 255 " pdb=" CG1 VAL A 255 " pdb=" CG2 VAL A 255 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 951 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 192 " -0.022 2.00e-02 2.50e+03 2.06e-02 7.41e+00 pdb=" CG PHE A 192 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 192 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 192 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 192 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 192 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 192 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 192 " 0.022 2.00e-02 2.50e+03 2.03e-02 7.23e+00 pdb=" CG PHE B 192 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 192 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 192 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 192 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 192 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 192 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 32 " 0.013 2.00e-02 2.50e+03 1.67e-02 4.90e+00 pdb=" CG PHE A 32 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 32 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 32 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 32 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 32 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 32 " 0.001 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 148 2.63 - 3.20: 6423 3.20 - 3.76: 10358 3.76 - 4.33: 15209 4.33 - 4.90: 23412 Nonbonded interactions: 55550 Sorted by model distance: nonbonded pdb=" NZ LYS A 29 " pdb=" OD1 ASP A 399 " model vdw 2.061 3.120 nonbonded pdb=" NZ LYS B 29 " pdb=" OD1 ASP B 399 " model vdw 2.061 3.120 nonbonded pdb=" ND2 ASN B 184 " pdb=" OH TYR B 219 " model vdw 2.137 3.120 nonbonded pdb=" ND2 ASN A 184 " pdb=" OH TYR A 219 " model vdw 2.138 3.120 nonbonded pdb=" ND2 ASN B 116 " pdb=" O ILE B 367 " model vdw 2.148 3.120 ... (remaining 55545 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.620 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.660 Find NCS groups from input model: 0.110 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 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 : 0.012 0.223 6470 Z= 0.493 Angle : 1.235 16.593 8736 Z= 0.649 Chirality : 0.059 0.251 954 Planarity : 0.006 0.050 1104 Dihedral : 12.123 146.105 2378 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 29.53 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.14 % Favored : 93.35 % Rotamer: Outliers : 0.30 % Allowed : 1.21 % Favored : 98.49 % 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: -4.89 (0.22), residues: 782 helix: -3.96 (0.17), residues: 326 sheet: -2.87 (0.31), residues: 144 loop : -2.27 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP A 92 HIS 0.012 0.004 HIS B 170 PHE 0.047 0.005 PHE A 192 TYR 0.035 0.004 TYR B 231 ARG 0.011 0.002 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.32255 ( 302) hydrogen bonds : angle 12.62400 ( 900) covalent geometry : bond 0.01186 ( 6470) covalent geometry : angle 1.23492 ( 8736) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 VAL cc_start: 0.8490 (m) cc_final: 0.8000 (p) REVERT: A 257 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8344 (tp-100) REVERT: B 255 VAL cc_start: 0.8493 (m) cc_final: 0.8022 (p) REVERT: B 257 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8323 (tp-100) outliers start: 2 outliers final: 0 residues processed: 205 average time/residue: 0.2862 time to fit residues: 70.4416 Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 96 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN A 228 GLN A 271 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS A 385 ASN B 40 HIS B 96 ASN ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN B 228 GLN B 271 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS B 385 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.062968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050108 restraints weight = 29303.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.051917 restraints weight = 19828.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.053334 restraints weight = 14667.925| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6470 Z= 0.225 Angle : 0.844 6.363 8736 Z= 0.445 Chirality : 0.050 0.206 954 Planarity : 0.005 0.050 1104 Dihedral : 10.862 152.241 860 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.91 % Allowed : 12.84 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.26), residues: 782 helix: -1.50 (0.23), residues: 364 sheet: -2.34 (0.30), residues: 192 loop : -0.97 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP B 23 HIS 0.009 0.002 HIS B 248 PHE 0.022 0.003 PHE B 227 TYR 0.019 0.002 TYR A 219 ARG 0.004 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.05991 ( 302) hydrogen bonds : angle 6.82007 ( 900) covalent geometry : bond 0.00505 ( 6470) covalent geometry : angle 0.84418 ( 8736) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.9158 (tpt) cc_final: 0.8880 (tpt) REVERT: A 254 MET cc_start: 0.8440 (tpp) cc_final: 0.7966 (tpp) REVERT: A 255 VAL cc_start: 0.9684 (m) cc_final: 0.9214 (p) REVERT: A 257 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8467 (tm-30) REVERT: A 365 GLU cc_start: 0.8932 (pp20) cc_final: 0.8632 (pp20) REVERT: B 254 MET cc_start: 0.8427 (tpp) cc_final: 0.7964 (tpp) REVERT: B 255 VAL cc_start: 0.9678 (m) cc_final: 0.9204 (p) REVERT: B 257 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8470 (tm-30) outliers start: 6 outliers final: 4 residues processed: 130 average time/residue: 0.2218 time to fit residues: 36.6472 Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 101 ASN A 309 HIS B 68 ASN B 101 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.049407 restraints weight = 31151.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.051227 restraints weight = 20306.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.052648 restraints weight = 14613.786| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6470 Z= 0.177 Angle : 0.771 6.669 8736 Z= 0.401 Chirality : 0.047 0.174 954 Planarity : 0.004 0.039 1104 Dihedral : 10.195 151.004 860 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.02 % Allowed : 13.75 % Favored : 83.23 % 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: -1.43 (0.29), residues: 782 helix: -0.45 (0.26), residues: 366 sheet: -1.83 (0.33), residues: 188 loop : -0.50 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 23 HIS 0.005 0.002 HIS B 248 PHE 0.021 0.002 PHE A 355 TYR 0.017 0.002 TYR A 219 ARG 0.003 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 302) hydrogen bonds : angle 5.94324 ( 900) covalent geometry : bond 0.00407 ( 6470) covalent geometry : angle 0.77141 ( 8736) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.9245 (mmtp) cc_final: 0.9027 (mmtp) REVERT: A 254 MET cc_start: 0.8177 (tpp) cc_final: 0.6972 (tpp) REVERT: A 255 VAL cc_start: 0.9675 (m) cc_final: 0.9118 (p) REVERT: A 293 SER cc_start: 0.9310 (t) cc_final: 0.8320 (m) REVERT: A 396 GLU cc_start: 0.9390 (mt-10) cc_final: 0.8999 (mt-10) REVERT: B 254 MET cc_start: 0.8175 (tpp) cc_final: 0.7386 (tpp) REVERT: B 293 SER cc_start: 0.8706 (t) cc_final: 0.8502 (m) REVERT: B 396 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9083 (mt-10) outliers start: 20 outliers final: 6 residues processed: 140 average time/residue: 0.2217 time to fit residues: 39.2427 Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 50 optimal weight: 0.0070 chunk 10 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 overall best weight: 3.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.062500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050309 restraints weight = 30755.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052164 restraints weight = 19911.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053585 restraints weight = 14284.167| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6470 Z= 0.164 Angle : 0.768 6.865 8736 Z= 0.395 Chirality : 0.049 0.338 954 Planarity : 0.004 0.044 1104 Dihedral : 9.886 151.328 860 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.21 % Allowed : 18.58 % Favored : 80.21 % 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 (0.30), residues: 782 helix: 0.03 (0.27), residues: 366 sheet: -1.44 (0.36), residues: 180 loop : -0.27 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 23 HIS 0.004 0.002 HIS A 342 PHE 0.019 0.002 PHE A 227 TYR 0.013 0.001 TYR B 219 ARG 0.012 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 302) hydrogen bonds : angle 5.50021 ( 900) covalent geometry : bond 0.00384 ( 6470) covalent geometry : angle 0.76832 ( 8736) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 VAL cc_start: 0.9684 (m) cc_final: 0.9334 (p) REVERT: A 396 GLU cc_start: 0.9379 (mt-10) cc_final: 0.8979 (mt-10) REVERT: B 13 MET cc_start: 0.8938 (mmt) cc_final: 0.8691 (mmp) REVERT: B 18 MET cc_start: 0.9062 (ttm) cc_final: 0.8724 (ttm) REVERT: B 203 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8849 (tttm) REVERT: B 293 SER cc_start: 0.8723 (t) cc_final: 0.8436 (m) REVERT: B 396 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9003 (mt-10) outliers start: 8 outliers final: 2 residues processed: 118 average time/residue: 0.2206 time to fit residues: 33.1909 Evaluate side-chains 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 61 optimal weight: 0.0870 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS B 213 ASN B 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.062012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050562 restraints weight = 31396.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.052343 restraints weight = 20482.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.053685 restraints weight = 14740.708| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6470 Z= 0.158 Angle : 0.726 6.859 8736 Z= 0.373 Chirality : 0.047 0.251 954 Planarity : 0.004 0.047 1104 Dihedral : 9.566 148.118 860 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.51 % Allowed : 19.34 % Favored : 79.15 % 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: -0.25 (0.31), residues: 782 helix: 0.47 (0.28), residues: 366 sheet: -0.97 (0.39), residues: 164 loop : -0.26 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 23 HIS 0.011 0.002 HIS A 342 PHE 0.015 0.002 PHE A 355 TYR 0.013 0.001 TYR A 219 ARG 0.005 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 302) hydrogen bonds : angle 5.30067 ( 900) covalent geometry : bond 0.00369 ( 6470) covalent geometry : angle 0.72612 ( 8736) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8704 (mmmm) REVERT: A 13 MET cc_start: 0.9026 (mmp) cc_final: 0.8763 (mmp) REVERT: A 44 LEU cc_start: 0.9386 (mm) cc_final: 0.8646 (mm) REVERT: A 96 ASN cc_start: 0.9459 (OUTLIER) cc_final: 0.9233 (m110) REVERT: A 254 MET cc_start: 0.9062 (mtp) cc_final: 0.8837 (mtp) REVERT: A 255 VAL cc_start: 0.9718 (m) cc_final: 0.9421 (p) REVERT: A 260 LYS cc_start: 0.9265 (pttm) cc_final: 0.8847 (tptt) REVERT: A 342 HIS cc_start: 0.8540 (t70) cc_final: 0.8164 (t70) REVERT: A 396 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9041 (mt-10) REVERT: B 203 LYS cc_start: 0.9266 (mtpp) cc_final: 0.8976 (tptm) REVERT: B 254 MET cc_start: 0.8508 (tpp) cc_final: 0.8218 (tpt) REVERT: B 342 HIS cc_start: 0.8582 (t70) cc_final: 0.8189 (t70) REVERT: B 396 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9056 (mt-10) outliers start: 10 outliers final: 5 residues processed: 116 average time/residue: 0.2003 time to fit residues: 30.0532 Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 252 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 39 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 chunk 42 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 72 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.059688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.048408 restraints weight = 31478.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050057 restraints weight = 20285.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051346 restraints weight = 14670.049| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6470 Z= 0.187 Angle : 0.721 8.119 8736 Z= 0.371 Chirality : 0.046 0.206 954 Planarity : 0.004 0.030 1104 Dihedral : 9.372 143.903 860 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.51 % Allowed : 20.09 % Favored : 78.40 % 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: -0.23 (0.31), residues: 782 helix: 0.61 (0.28), residues: 372 sheet: -1.00 (0.39), residues: 160 loop : -0.48 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 23 HIS 0.005 0.001 HIS A 342 PHE 0.018 0.002 PHE B 397 TYR 0.010 0.002 TYR A 34 ARG 0.002 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 302) hydrogen bonds : angle 5.28608 ( 900) covalent geometry : bond 0.00424 ( 6470) covalent geometry : angle 0.72058 ( 8736) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.9014 (mmt) cc_final: 0.8371 (mmp) REVERT: A 23 TRP cc_start: 0.9066 (t-100) cc_final: 0.8377 (t-100) REVERT: A 44 LEU cc_start: 0.9358 (mm) cc_final: 0.8499 (mm) REVERT: A 254 MET cc_start: 0.9127 (mtp) cc_final: 0.8841 (mtp) REVERT: A 255 VAL cc_start: 0.9714 (m) cc_final: 0.9260 (p) REVERT: A 260 LYS cc_start: 0.9240 (pttm) cc_final: 0.9022 (pttm) REVERT: A 342 HIS cc_start: 0.8827 (t70) cc_final: 0.8354 (t70) REVERT: A 396 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9129 (mt-10) REVERT: B 23 TRP cc_start: 0.9199 (t-100) cc_final: 0.8544 (t-100) REVERT: B 44 LEU cc_start: 0.9365 (mm) cc_final: 0.8755 (mm) REVERT: B 130 ILE cc_start: 0.9386 (mp) cc_final: 0.9080 (tt) REVERT: B 203 LYS cc_start: 0.9257 (mtpp) cc_final: 0.8990 (tptm) REVERT: B 342 HIS cc_start: 0.8848 (t70) cc_final: 0.8375 (t70) REVERT: B 396 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9120 (mt-10) outliers start: 10 outliers final: 7 residues processed: 107 average time/residue: 0.2194 time to fit residues: 30.2360 Evaluate side-chains 96 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.058812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.047705 restraints weight = 31885.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049364 restraints weight = 20677.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.050618 restraints weight = 14905.721| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6470 Z= 0.189 Angle : 0.723 10.389 8736 Z= 0.372 Chirality : 0.046 0.207 954 Planarity : 0.004 0.031 1104 Dihedral : 9.287 140.167 860 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.21 % Allowed : 20.85 % Favored : 77.95 % 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: -0.28 (0.31), residues: 782 helix: 0.69 (0.28), residues: 372 sheet: -1.30 (0.38), residues: 168 loop : -0.46 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 23 HIS 0.010 0.002 HIS B 248 PHE 0.015 0.002 PHE A 397 TYR 0.010 0.001 TYR A 34 ARG 0.003 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 302) hydrogen bonds : angle 5.30856 ( 900) covalent geometry : bond 0.00429 ( 6470) covalent geometry : angle 0.72268 ( 8736) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.9000 (mmt) cc_final: 0.8379 (mmp) REVERT: A 23 TRP cc_start: 0.8882 (t-100) cc_final: 0.8246 (t-100) REVERT: A 44 LEU cc_start: 0.9350 (mm) cc_final: 0.8503 (mm) REVERT: A 96 ASN cc_start: 0.9427 (OUTLIER) cc_final: 0.9182 (m110) REVERT: A 254 MET cc_start: 0.9234 (mtp) cc_final: 0.8863 (mtp) REVERT: A 342 HIS cc_start: 0.8843 (t70) cc_final: 0.8365 (t70) REVERT: A 396 GLU cc_start: 0.9496 (mt-10) cc_final: 0.9188 (mt-10) REVERT: B 44 LEU cc_start: 0.9368 (mm) cc_final: 0.8604 (mm) REVERT: B 130 ILE cc_start: 0.9361 (mp) cc_final: 0.9059 (tt) REVERT: B 203 LYS cc_start: 0.9294 (mtpp) cc_final: 0.9022 (tptm) REVERT: B 342 HIS cc_start: 0.8862 (t70) cc_final: 0.8403 (t70) REVERT: B 396 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9159 (mt-10) outliers start: 8 outliers final: 7 residues processed: 109 average time/residue: 0.2101 time to fit residues: 29.4289 Evaluate side-chains 101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 16 optimal weight: 0.1980 chunk 18 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 40.0000 chunk 7 optimal weight: 7.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.059303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048234 restraints weight = 31543.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.049920 restraints weight = 20145.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051165 restraints weight = 14387.984| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.7178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6470 Z= 0.169 Angle : 0.761 8.735 8736 Z= 0.379 Chirality : 0.045 0.208 954 Planarity : 0.004 0.034 1104 Dihedral : 9.239 138.316 860 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.06 % Allowed : 22.36 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.31), residues: 782 helix: 0.67 (0.28), residues: 372 sheet: -1.27 (0.38), residues: 164 loop : -0.39 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 23 HIS 0.009 0.002 HIS B 248 PHE 0.014 0.002 PHE B 397 TYR 0.011 0.001 TYR B 34 ARG 0.008 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 302) hydrogen bonds : angle 5.15512 ( 900) covalent geometry : bond 0.00393 ( 6470) covalent geometry : angle 0.76078 ( 8736) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8998 (mmt) cc_final: 0.8507 (mmp) REVERT: A 18 MET cc_start: 0.8967 (ttm) cc_final: 0.8732 (ptm) REVERT: A 44 LEU cc_start: 0.9342 (mm) cc_final: 0.8468 (mm) REVERT: A 254 MET cc_start: 0.9291 (mtp) cc_final: 0.8854 (mtp) REVERT: A 342 HIS cc_start: 0.8846 (t70) cc_final: 0.8360 (t70) REVERT: A 396 GLU cc_start: 0.9486 (mt-10) cc_final: 0.9177 (mt-10) REVERT: B 44 LEU cc_start: 0.9360 (mm) cc_final: 0.8699 (mm) REVERT: B 130 ILE cc_start: 0.9334 (mp) cc_final: 0.9053 (tt) REVERT: B 203 LYS cc_start: 0.9321 (mtpp) cc_final: 0.9009 (tptm) REVERT: B 342 HIS cc_start: 0.8897 (t70) cc_final: 0.8428 (t70) REVERT: B 396 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9181 (mt-10) outliers start: 7 outliers final: 7 residues processed: 108 average time/residue: 0.2536 time to fit residues: 35.8991 Evaluate side-chains 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.059696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.048698 restraints weight = 32633.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.050350 restraints weight = 21093.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.051647 restraints weight = 15233.018| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6470 Z= 0.163 Angle : 0.786 14.335 8736 Z= 0.386 Chirality : 0.046 0.217 954 Planarity : 0.004 0.031 1104 Dihedral : 9.123 135.053 860 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.21 % Allowed : 22.36 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.31 (0.31), residues: 782 helix: 0.65 (0.27), residues: 376 sheet: -1.30 (0.38), residues: 168 loop : -0.46 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 23 HIS 0.008 0.001 HIS B 248 PHE 0.016 0.002 PHE B 397 TYR 0.015 0.001 TYR B 208 ARG 0.007 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 302) hydrogen bonds : angle 5.11527 ( 900) covalent geometry : bond 0.00381 ( 6470) covalent geometry : angle 0.78619 ( 8736) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8928 (mmt) cc_final: 0.8368 (mmp) REVERT: A 44 LEU cc_start: 0.9320 (mm) cc_final: 0.8414 (mm) REVERT: A 96 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.9094 (m110) REVERT: A 254 MET cc_start: 0.9215 (mtp) cc_final: 0.8783 (mtp) REVERT: A 342 HIS cc_start: 0.8816 (t70) cc_final: 0.8367 (t70) REVERT: A 396 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9164 (mt-10) REVERT: B 44 LEU cc_start: 0.9347 (mm) cc_final: 0.8717 (mm) REVERT: B 130 ILE cc_start: 0.9331 (mp) cc_final: 0.9027 (tt) REVERT: B 203 LYS cc_start: 0.9230 (mtpp) cc_final: 0.8933 (tptm) REVERT: B 342 HIS cc_start: 0.8850 (t70) cc_final: 0.8438 (t70) REVERT: B 396 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9177 (mt-10) outliers start: 8 outliers final: 7 residues processed: 108 average time/residue: 0.1869 time to fit residues: 26.7630 Evaluate side-chains 105 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.058443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.047478 restraints weight = 32532.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.049069 restraints weight = 21283.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050287 restraints weight = 15474.227| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.7504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6470 Z= 0.196 Angle : 0.802 14.380 8736 Z= 0.397 Chirality : 0.046 0.215 954 Planarity : 0.004 0.030 1104 Dihedral : 9.079 133.250 860 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.21 % Allowed : 23.11 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.26 (0.31), residues: 782 helix: 0.70 (0.28), residues: 372 sheet: -1.28 (0.38), residues: 160 loop : -0.49 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 23 HIS 0.010 0.002 HIS B 248 PHE 0.019 0.002 PHE B 397 TYR 0.013 0.002 TYR B 208 ARG 0.008 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 302) hydrogen bonds : angle 5.15690 ( 900) covalent geometry : bond 0.00452 ( 6470) covalent geometry : angle 0.80240 ( 8736) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8942 (mmt) cc_final: 0.8385 (mmp) REVERT: A 44 LEU cc_start: 0.9312 (mm) cc_final: 0.8414 (mm) REVERT: A 96 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.9063 (m110) REVERT: A 254 MET cc_start: 0.9204 (mtp) cc_final: 0.8771 (mtp) REVERT: A 342 HIS cc_start: 0.8827 (t70) cc_final: 0.8397 (t70) REVERT: A 396 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9196 (mt-10) REVERT: B 44 LEU cc_start: 0.9328 (mm) cc_final: 0.8697 (mm) REVERT: B 203 LYS cc_start: 0.9226 (mtpp) cc_final: 0.8946 (tptm) REVERT: B 342 HIS cc_start: 0.8871 (t70) cc_final: 0.8470 (t70) REVERT: B 398 MET cc_start: 0.9233 (mmm) cc_final: 0.9024 (tpt) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.2019 time to fit residues: 26.5385 Evaluate side-chains 98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 28 optimal weight: 50.0000 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.058508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.047445 restraints weight = 32641.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.049078 restraints weight = 21333.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.050241 restraints weight = 15439.348| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6470 Z= 0.198 Angle : 0.813 13.926 8736 Z= 0.403 Chirality : 0.047 0.215 954 Planarity : 0.003 0.026 1104 Dihedral : 9.061 131.114 860 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.21 % Allowed : 22.96 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.41 (0.30), residues: 782 helix: 0.57 (0.27), residues: 376 sheet: -1.35 (0.38), residues: 164 loop : -0.54 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 267 HIS 0.015 0.002 HIS A 248 PHE 0.016 0.002 PHE A 397 TYR 0.015 0.002 TYR B 208 ARG 0.006 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 302) hydrogen bonds : angle 5.23972 ( 900) covalent geometry : bond 0.00459 ( 6470) covalent geometry : angle 0.81289 ( 8736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2726.40 seconds wall clock time: 48 minutes 49.96 seconds (2929.96 seconds total)