Starting phenix.real_space_refine on Thu Feb 5 08:17:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irp_35682/02_2026/8irp_35682_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irp_35682/02_2026/8irp_35682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8irp_35682/02_2026/8irp_35682_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irp_35682/02_2026/8irp_35682_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8irp_35682/02_2026/8irp_35682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irp_35682/02_2026/8irp_35682.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 S 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1474 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16350 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'H35': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'H35': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.17, per 1000 atoms: 0.19 Number of scatterers: 16350 At special positions: 0 Unit cell: (94.461, 109.779, 101.269, 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 52 16.00 O 1474 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 556.1 milliseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 68.5% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 73 removed outlier: 4.233A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 149 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.855A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.618A pdb=" N LEU B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.331A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.933A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.668A pdb=" N ILE B 374 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN B 375 " --> pdb=" O SER B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 375' Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.687A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.007A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 495 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 496 through 502 removed outlier: 3.530A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.834A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 554 removed outlier: 4.619A pdb=" N TRP B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.233A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 149 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.855A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.618A pdb=" N LEU A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.332A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.933A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.668A pdb=" N ILE A 374 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN A 375 " --> pdb=" O SER A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 375' Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.687A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.007A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 495 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.530A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix removed outlier: 3.833A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 4.619A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.685A pdb=" N SER B 274 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 274 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.819A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 158 510 hydrogen bonds defined for protein. 1446 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: 3.51 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: 0.84 - 1.03: 8204 1.03 - 1.23: 14 1.23 - 1.42: 3412 1.42 - 1.62: 4824 1.62 - 1.81: 84 Bond restraints: 16538 Sorted by residual: bond pdb=" C6 H35 A 701 " pdb=" N6 H35 A 701 " ideal model delta sigma weight residual 1.345 1.447 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C6 H35 B 701 " pdb=" N6 H35 B 701 " ideal model delta sigma weight residual 1.345 1.447 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" CAM H35 B 701 " pdb=" CAO H35 B 701 " ideal model delta sigma weight residual 1.429 1.386 0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" CAM H35 A 701 " pdb=" CAO H35 A 701 " ideal model delta sigma weight residual 1.429 1.386 0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 16533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 29627 1.81 - 3.62: 251 3.62 - 5.43: 38 5.43 - 7.24: 4 7.24 - 9.05: 6 Bond angle restraints: 29926 Sorted by residual: angle pdb=" N LEU B 248 " pdb=" CA LEU B 248 " pdb=" CB LEU B 248 " ideal model delta sigma weight residual 114.17 110.08 4.09 1.14e+00 7.69e-01 1.29e+01 angle pdb=" N LEU A 248 " pdb=" CA LEU A 248 " pdb=" CB LEU A 248 " ideal model delta sigma weight residual 114.17 110.09 4.08 1.14e+00 7.69e-01 1.28e+01 angle pdb=" C2 H35 A 701 " pdb=" N3 H35 A 701 " pdb=" C4 H35 A 701 " ideal model delta sigma weight residual 113.07 122.12 -9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" C2 H35 B 701 " pdb=" N3 H35 B 701 " pdb=" C4 H35 B 701 " ideal model delta sigma weight residual 113.07 122.11 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" CAP H35 A 701 " pdb=" CAK H35 A 701 " pdb=" OAL H35 A 701 " ideal model delta sigma weight residual 118.02 126.33 -8.31 3.00e+00 1.11e-01 7.67e+00 ... (remaining 29921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.96: 7461 24.96 - 49.93: 296 49.93 - 74.89: 117 74.89 - 99.86: 4 99.86 - 124.82: 2 Dihedral angle restraints: 7880 sinusoidal: 4246 harmonic: 3634 Sorted by residual: dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 143.50 36.50 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 143.56 36.44 0 5.00e+00 4.00e-02 5.31e+01 dihedral pdb=" CA PHE B 332 " pdb=" C PHE B 332 " pdb=" N ARG B 333 " pdb=" CA ARG B 333 " ideal model delta harmonic sigma weight residual 180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1324 0.099 - 0.199: 31 0.199 - 0.298: 0 0.298 - 0.398: 0 0.398 - 0.497: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 270 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA ILE A 266 " pdb=" N ILE A 266 " pdb=" C ILE A 266 " pdb=" CB ILE A 266 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 270 " -0.094 2.00e-02 2.50e+03 7.85e-02 9.25e+01 pdb=" CG ASN B 270 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 270 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B 270 " 0.085 2.00e-02 2.50e+03 pdb="HD21 ASN B 270 " 0.065 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 487 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO A 487 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.033 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 122 1.98 - 2.63: 21588 2.63 - 3.29: 52563 3.29 - 3.94: 67232 3.94 - 4.60: 105585 Nonbonded interactions: 247090 Sorted by model distance: nonbonded pdb="HG23 THR A 162 " pdb=" HE1 PHE A 386 " model vdw 1.324 2.270 nonbonded pdb="HG21 THR A 162 " pdb=" HD2 PRO A 438 " model vdw 1.376 2.440 nonbonded pdb=" OD1 ASP A 130 " pdb=" HE2 HIS A 360 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP B 130 " pdb=" HE2 HIS B 360 " model vdw 1.603 2.450 nonbonded pdb="HH22 ARG B 333 " pdb=" OD1 ASP B 347 " model vdw 1.606 2.450 ... (remaining 247085 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.940 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: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.710 Find NCS groups from input model: 0.200 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.004 0.102 8342 Z= 0.197 Angle : 0.645 12.829 11366 Z= 0.318 Chirality : 0.042 0.497 1356 Planarity : 0.004 0.058 1400 Dihedral : 13.359 124.823 2936 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1076 helix: 1.78 (0.20), residues: 654 sheet: -5.81 (0.22), residues: 20 loop : -0.48 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 454 TYR 0.010 0.001 TYR B 524 PHE 0.022 0.001 PHE A 203 TRP 0.008 0.001 TRP B 482 HIS 0.001 0.000 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8330) covalent geometry : angle 0.61162 (11338) SS BOND : bond 0.00162 ( 8) SS BOND : angle 1.32796 ( 16) hydrogen bonds : bond 0.10724 ( 506) hydrogen bonds : angle 4.97067 ( 1446) link_BETA1-4 : bond 0.00442 ( 2) link_BETA1-4 : angle 2.61143 ( 6) link_NAG-ASN : bond 0.07830 ( 2) link_NAG-ASN : angle 8.30898 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.631 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 91 average time/residue: 1.1586 time to fit residues: 112.5904 Evaluate side-chains 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.097488 restraints weight = 28596.749| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.57 r_work: 0.2845 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8342 Z= 0.170 Angle : 0.559 7.706 11366 Z= 0.294 Chirality : 0.040 0.144 1356 Planarity : 0.004 0.058 1400 Dihedral : 8.128 109.086 1238 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.70 % Allowed : 4.78 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1076 helix: 1.78 (0.20), residues: 648 sheet: -5.74 (0.29), residues: 20 loop : -0.57 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.010 0.001 TYR B 388 PHE 0.012 0.002 PHE A 166 TRP 0.007 0.001 TRP A 380 HIS 0.002 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8330) covalent geometry : angle 0.55075 (11338) SS BOND : bond 0.00155 ( 8) SS BOND : angle 1.49322 ( 16) hydrogen bonds : bond 0.04677 ( 506) hydrogen bonds : angle 4.47767 ( 1446) link_BETA1-4 : bond 0.00542 ( 2) link_BETA1-4 : angle 3.08136 ( 6) link_NAG-ASN : bond 0.00035 ( 2) link_NAG-ASN : angle 2.06971 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.658 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 81 average time/residue: 1.2204 time to fit residues: 105.5765 Evaluate side-chains 79 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain A residue 126 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.088676 restraints weight = 29645.605| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.67 r_work: 0.2832 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8342 Z= 0.156 Angle : 0.547 9.304 11366 Z= 0.283 Chirality : 0.040 0.156 1356 Planarity : 0.004 0.059 1400 Dihedral : 7.437 95.981 1234 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.70 % Allowed : 6.88 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.26), residues: 1076 helix: 1.77 (0.20), residues: 648 sheet: -5.45 (0.42), residues: 20 loop : -0.59 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.010 0.001 TYR B 388 PHE 0.016 0.001 PHE A 203 TRP 0.007 0.001 TRP A 482 HIS 0.002 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8330) covalent geometry : angle 0.53778 (11338) SS BOND : bond 0.00183 ( 8) SS BOND : angle 1.44602 ( 16) hydrogen bonds : bond 0.04368 ( 506) hydrogen bonds : angle 4.35468 ( 1446) link_BETA1-4 : bond 0.00420 ( 2) link_BETA1-4 : angle 3.30900 ( 6) link_NAG-ASN : bond 0.00136 ( 2) link_NAG-ASN : angle 1.88381 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: B 494 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7232 (mpp) REVERT: A 494 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7228 (mpp) REVERT: A 509 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7527 (mt-10) outliers start: 6 outliers final: 2 residues processed: 78 average time/residue: 1.2812 time to fit residues: 106.3748 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.090378 restraints weight = 29343.472| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.66 r_work: 0.2853 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8342 Z= 0.122 Angle : 0.528 10.782 11366 Z= 0.270 Chirality : 0.039 0.130 1356 Planarity : 0.004 0.059 1400 Dihedral : 6.694 79.916 1234 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.93 % Allowed : 6.99 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1076 helix: 1.92 (0.20), residues: 654 sheet: -5.39 (0.45), residues: 20 loop : -0.54 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 23 TYR 0.009 0.001 TYR B 388 PHE 0.017 0.001 PHE B 203 TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8330) covalent geometry : angle 0.51785 (11338) SS BOND : bond 0.00171 ( 8) SS BOND : angle 1.24609 ( 16) hydrogen bonds : bond 0.03964 ( 506) hydrogen bonds : angle 4.23190 ( 1446) link_BETA1-4 : bond 0.00372 ( 2) link_BETA1-4 : angle 3.57210 ( 6) link_NAG-ASN : bond 0.00184 ( 2) link_NAG-ASN : angle 1.90467 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7200 (mpp) REVERT: B 520 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8481 (mtt) REVERT: A 494 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7172 (mpp) REVERT: A 509 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7501 (mt-10) REVERT: A 520 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8446 (mtt) outliers start: 8 outliers final: 0 residues processed: 83 average time/residue: 1.2316 time to fit residues: 109.2159 Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 520 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.089577 restraints weight = 29264.604| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.66 r_work: 0.2841 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8342 Z= 0.148 Angle : 0.546 11.115 11366 Z= 0.279 Chirality : 0.040 0.129 1356 Planarity : 0.004 0.059 1400 Dihedral : 5.863 53.710 1234 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.35 % Allowed : 8.62 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.26), residues: 1076 helix: 1.90 (0.20), residues: 646 sheet: -5.31 (0.47), residues: 20 loop : -0.57 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.009 0.001 TYR B 388 PHE 0.018 0.002 PHE A 203 TRP 0.007 0.001 TRP B 482 HIS 0.002 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8330) covalent geometry : angle 0.53312 (11338) SS BOND : bond 0.00197 ( 8) SS BOND : angle 1.41039 ( 16) hydrogen bonds : bond 0.04150 ( 506) hydrogen bonds : angle 4.21735 ( 1446) link_BETA1-4 : bond 0.00229 ( 2) link_BETA1-4 : angle 4.34208 ( 6) link_NAG-ASN : bond 0.00112 ( 2) link_NAG-ASN : angle 2.01536 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7199 (mpp) REVERT: A 494 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7205 (mpp) REVERT: A 509 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7547 (mt-10) outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 1.1772 time to fit residues: 100.6102 Evaluate side-chains 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.090018 restraints weight = 29363.981| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.68 r_work: 0.2848 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8342 Z= 0.118 Angle : 0.520 8.351 11366 Z= 0.266 Chirality : 0.039 0.132 1356 Planarity : 0.004 0.059 1400 Dihedral : 5.172 48.058 1234 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.35 % Allowed : 9.32 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.26), residues: 1076 helix: 1.99 (0.20), residues: 646 sheet: -5.36 (0.46), residues: 20 loop : -0.52 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.009 0.001 TYR B 388 PHE 0.015 0.001 PHE B 203 TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8330) covalent geometry : angle 0.50431 (11338) SS BOND : bond 0.00157 ( 8) SS BOND : angle 1.22131 ( 16) hydrogen bonds : bond 0.03914 ( 506) hydrogen bonds : angle 4.16853 ( 1446) link_BETA1-4 : bond 0.00308 ( 2) link_BETA1-4 : angle 4.83539 ( 6) link_NAG-ASN : bond 0.00148 ( 2) link_NAG-ASN : angle 2.28324 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7197 (mpp) REVERT: A 494 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7219 (mpp) REVERT: A 509 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7488 (mt-10) outliers start: 3 outliers final: 1 residues processed: 79 average time/residue: 1.2500 time to fit residues: 105.4133 Evaluate side-chains 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.088131 restraints weight = 29426.142| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.65 r_work: 0.2821 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8342 Z= 0.198 Angle : 0.561 8.473 11366 Z= 0.292 Chirality : 0.041 0.149 1356 Planarity : 0.005 0.059 1400 Dihedral : 5.214 46.686 1234 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 0.82 % Allowed : 9.91 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1076 helix: 1.77 (0.20), residues: 646 sheet: -5.28 (0.47), residues: 20 loop : -0.64 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 23 TYR 0.010 0.002 TYR B 388 PHE 0.017 0.002 PHE B 203 TRP 0.006 0.001 TRP B 482 HIS 0.002 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8330) covalent geometry : angle 0.54412 (11338) SS BOND : bond 0.00214 ( 8) SS BOND : angle 1.67948 ( 16) hydrogen bonds : bond 0.04412 ( 506) hydrogen bonds : angle 4.26922 ( 1446) link_BETA1-4 : bond 0.00217 ( 2) link_BETA1-4 : angle 4.69471 ( 6) link_NAG-ASN : bond 0.00132 ( 2) link_NAG-ASN : angle 2.50363 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7301 (mpp) REVERT: A 494 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7297 (mpp) REVERT: A 509 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7572 (mt-10) outliers start: 7 outliers final: 3 residues processed: 78 average time/residue: 1.2985 time to fit residues: 108.0290 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.089246 restraints weight = 29244.569| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.66 r_work: 0.2831 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8342 Z= 0.143 Angle : 0.528 7.777 11366 Z= 0.273 Chirality : 0.039 0.149 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.118 46.486 1234 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.47 % Allowed : 10.37 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1076 helix: 1.88 (0.20), residues: 646 sheet: -5.32 (0.47), residues: 20 loop : -0.65 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 23 TYR 0.009 0.001 TYR B 388 PHE 0.017 0.001 PHE B 203 TRP 0.007 0.001 TRP A 482 HIS 0.002 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8330) covalent geometry : angle 0.51270 (11338) SS BOND : bond 0.00167 ( 8) SS BOND : angle 1.40133 ( 16) hydrogen bonds : bond 0.04084 ( 506) hydrogen bonds : angle 4.21907 ( 1446) link_BETA1-4 : bond 0.00155 ( 2) link_BETA1-4 : angle 4.38873 ( 6) link_NAG-ASN : bond 0.00161 ( 2) link_NAG-ASN : angle 2.43698 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7275 (mpp) REVERT: A 494 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7270 (mpp) REVERT: A 509 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7554 (mt-10) outliers start: 4 outliers final: 2 residues processed: 79 average time/residue: 1.3074 time to fit residues: 110.2743 Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 61 optimal weight: 0.0070 chunk 62 optimal weight: 5.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.113944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.091885 restraints weight = 29218.893| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.66 r_work: 0.2883 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8342 Z= 0.108 Angle : 0.503 6.894 11366 Z= 0.259 Chirality : 0.039 0.143 1356 Planarity : 0.004 0.060 1400 Dihedral : 4.906 45.552 1234 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.23 % Allowed : 10.61 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.26), residues: 1076 helix: 2.07 (0.20), residues: 646 sheet: -5.39 (0.44), residues: 20 loop : -0.50 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 23 TYR 0.008 0.001 TYR A 388 PHE 0.014 0.001 PHE A 555 TRP 0.008 0.001 TRP B 482 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8330) covalent geometry : angle 0.49080 (11338) SS BOND : bond 0.00171 ( 8) SS BOND : angle 1.17662 ( 16) hydrogen bonds : bond 0.03738 ( 506) hydrogen bonds : angle 4.11716 ( 1446) link_BETA1-4 : bond 0.00129 ( 2) link_BETA1-4 : angle 3.97481 ( 6) link_NAG-ASN : bond 0.00215 ( 2) link_NAG-ASN : angle 2.27163 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7222 (mpp) REVERT: A 494 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7196 (mpp) REVERT: A 509 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7529 (mt-10) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 1.2314 time to fit residues: 105.2609 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.090527 restraints weight = 29245.173| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.66 r_work: 0.2860 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8342 Z= 0.135 Angle : 0.524 8.619 11366 Z= 0.269 Chirality : 0.039 0.147 1356 Planarity : 0.004 0.059 1400 Dihedral : 4.936 45.211 1234 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.35 % Allowed : 10.72 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.26), residues: 1076 helix: 2.05 (0.20), residues: 646 sheet: -5.35 (0.44), residues: 20 loop : -0.51 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.009 0.001 TYR A 388 PHE 0.016 0.001 PHE B 203 TRP 0.007 0.001 TRP A 482 HIS 0.002 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8330) covalent geometry : angle 0.51174 (11338) SS BOND : bond 0.00180 ( 8) SS BOND : angle 1.30123 ( 16) hydrogen bonds : bond 0.03895 ( 506) hydrogen bonds : angle 4.10400 ( 1446) link_BETA1-4 : bond 0.00121 ( 2) link_BETA1-4 : angle 3.98966 ( 6) link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 2.11826 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7210 (mpp) REVERT: A 494 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7238 (mpp) REVERT: A 509 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7478 (mt-10) outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 1.2803 time to fit residues: 109.4164 Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.090665 restraints weight = 29203.772| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.65 r_work: 0.2855 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8342 Z= 0.134 Angle : 0.523 8.419 11366 Z= 0.269 Chirality : 0.039 0.149 1356 Planarity : 0.004 0.059 1400 Dihedral : 4.943 44.920 1234 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.47 % Allowed : 10.49 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1076 helix: 2.03 (0.20), residues: 646 sheet: -5.35 (0.44), residues: 20 loop : -0.53 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.008 0.001 TYR B 388 PHE 0.014 0.001 PHE A 203 TRP 0.007 0.001 TRP A 482 HIS 0.001 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8330) covalent geometry : angle 0.51106 (11338) SS BOND : bond 0.00152 ( 8) SS BOND : angle 1.31943 ( 16) hydrogen bonds : bond 0.03919 ( 506) hydrogen bonds : angle 4.10882 ( 1446) link_BETA1-4 : bond 0.00106 ( 2) link_BETA1-4 : angle 4.00374 ( 6) link_NAG-ASN : bond 0.00149 ( 2) link_NAG-ASN : angle 2.06231 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.61 seconds wall clock time: 80 minutes 39.99 seconds (4839.99 seconds total)