Starting phenix.real_space_refine on Wed Mar 4 08:28:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dys_30924/03_2026/7dys_30924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dys_30924/03_2026/7dys_30924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dys_30924/03_2026/7dys_30924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dys_30924/03_2026/7dys_30924.map" model { file = "/net/cci-nas-00/data/ceres_data/7dys_30924/03_2026/7dys_30924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dys_30924/03_2026/7dys_30924.cif" } resolution = 3.18 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= 0.002 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7897 2.51 5 N 1919 2.21 5 O 2181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12065 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3012 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 382} Chain breaks: 7 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3022 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 382} Chain breaks: 7 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3018 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 382} Chain breaks: 7 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3013 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 382} Chain breaks: 7 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 2.35, per 1000 atoms: 0.19 Number of scatterers: 12065 At special positions: 0 Unit cell: (111.24, 111.24, 106.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2181 8.00 N 1919 7.00 C 7897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 243 " - pdb=" SG CYS D 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 557.0 milliseconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 65.5% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 66 through 106 removed outlier: 4.014A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 204 through 212 removed outlier: 6.761A pdb=" N SER A 209 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 210 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 211 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 377 through 397 Processing helix chain 'A' and resid 400 through 440 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.847A pdb=" N THR A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 517 removed outlier: 4.675A pdb=" N LEU A 501 " --> pdb=" O MET A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 106 removed outlier: 3.516A pdb=" N LYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 203 through 212 removed outlier: 6.839A pdb=" N SER B 209 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE B 210 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 346 through 366 Processing helix chain 'B' and resid 377 through 397 Processing helix chain 'B' and resid 400 through 440 Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.680A pdb=" N THR B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 517 removed outlier: 4.668A pdb=" N LEU B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 106 removed outlier: 4.015A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.507A pdb=" N GLN C 207 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 209 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE C 210 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 346 through 366 Processing helix chain 'C' and resid 377 through 397 Processing helix chain 'C' and resid 400 through 440 Proline residue: C 415 - end of helix Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.664A pdb=" N THR C 468 " --> pdb=" O ASP C 464 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 469 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 517 removed outlier: 4.670A pdb=" N LEU C 501 " --> pdb=" O MET C 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 106 removed outlier: 3.515A pdb=" N LYS D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.550A pdb=" N GLN D 207 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER D 209 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE D 210 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 346 through 366 Processing helix chain 'D' and resid 377 through 397 Processing helix chain 'D' and resid 400 through 440 Proline residue: D 415 - end of helix Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.721A pdb=" N THR D 468 " --> pdb=" O ASP D 464 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 469 " --> pdb=" O MET D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 517 removed outlier: 4.669A pdb=" N LEU D 501 " --> pdb=" O MET D 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 4.142A pdb=" N CYS A 119 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 removed outlier: 4.142A pdb=" N CYS A 119 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 218 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR A 168 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.140A pdb=" N CYS B 119 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.140A pdb=" N CYS B 119 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 218 " --> pdb=" O TYR B 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 168 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 121 removed outlier: 4.141A pdb=" N CYS C 119 " --> pdb=" O ILE C 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 removed outlier: 4.141A pdb=" N CYS C 119 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 218 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR C 168 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121 removed outlier: 4.140A pdb=" N CYS D 119 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 removed outlier: 4.140A pdb=" N CYS D 119 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 218 " --> pdb=" O TYR D 168 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR D 168 " --> pdb=" O LEU D 218 " (cutoff:3.500A) 985 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.25 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: 3661 1.34 - 1.46: 3149 1.46 - 1.59: 5395 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 12293 Sorted by residual: bond pdb=" C GLU B 201 " pdb=" N PRO B 202 " ideal model delta sigma weight residual 1.329 1.361 -0.032 1.25e-02 6.40e+03 6.58e+00 bond pdb=" CB THR B 127 " pdb=" CG2 THR B 127 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.38e+00 bond pdb=" CB THR A 127 " pdb=" CG2 THR A 127 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CB THR D 127 " pdb=" CG2 THR D 127 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CB THR C 127 " pdb=" CG2 THR C 127 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 ... (remaining 12288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 15710 1.69 - 3.37: 792 3.37 - 5.06: 118 5.06 - 6.74: 36 6.74 - 8.43: 22 Bond angle restraints: 16678 Sorted by residual: angle pdb=" C ILE C 437 " pdb=" N VAL C 438 " pdb=" CA VAL C 438 " ideal model delta sigma weight residual 122.97 118.96 4.01 9.80e-01 1.04e+00 1.67e+01 angle pdb=" C ILE D 437 " pdb=" N VAL D 438 " pdb=" CA VAL D 438 " ideal model delta sigma weight residual 122.97 118.99 3.98 9.80e-01 1.04e+00 1.65e+01 angle pdb=" C ILE B 437 " pdb=" N VAL B 438 " pdb=" CA VAL B 438 " ideal model delta sigma weight residual 122.97 119.00 3.97 9.80e-01 1.04e+00 1.64e+01 angle pdb=" C ILE A 437 " pdb=" N VAL A 438 " pdb=" CA VAL A 438 " ideal model delta sigma weight residual 122.97 119.06 3.91 9.80e-01 1.04e+00 1.59e+01 angle pdb=" N ASP A 204 " pdb=" CA ASP A 204 " pdb=" C ASP A 204 " ideal model delta sigma weight residual 113.55 109.06 4.49 1.26e+00 6.30e-01 1.27e+01 ... (remaining 16673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 6755 15.83 - 31.65: 317 31.65 - 47.48: 65 47.48 - 63.30: 11 63.30 - 79.13: 12 Dihedral angle restraints: 7160 sinusoidal: 2624 harmonic: 4536 Sorted by residual: dihedral pdb=" CA GLU A 201 " pdb=" C GLU A 201 " pdb=" N PRO A 202 " pdb=" CA PRO A 202 " ideal model delta harmonic sigma weight residual 180.00 131.48 48.52 0 5.00e+00 4.00e-02 9.42e+01 dihedral pdb=" CB CYS B 243 " pdb=" SG CYS B 243 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual -86.00 -158.42 72.42 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS C 243 " pdb=" SG CYS C 243 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual -86.00 -158.40 72.40 1 1.00e+01 1.00e-02 6.70e+01 ... (remaining 7157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1047 0.036 - 0.071: 625 0.071 - 0.107: 245 0.107 - 0.142: 64 0.142 - 0.178: 33 Chirality restraints: 2014 Sorted by residual: chirality pdb=" CA LEU C 414 " pdb=" N LEU C 414 " pdb=" C LEU C 414 " pdb=" CB LEU C 414 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA LEU D 414 " pdb=" N LEU D 414 " pdb=" C LEU D 414 " pdb=" CB LEU D 414 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CA LEU A 414 " pdb=" N LEU A 414 " pdb=" C LEU A 414 " pdb=" CB LEU A 414 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.58e-01 ... (remaining 2011 not shown) Planarity restraints: 2027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 201 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 202 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 495 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ILE A 495 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 495 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 496 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 495 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C ILE B 495 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 495 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 496 " 0.015 2.00e-02 2.50e+03 ... (remaining 2024 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3906 2.84 - 3.35: 11731 3.35 - 3.87: 20018 3.87 - 4.38: 22160 4.38 - 4.90: 38672 Nonbonded interactions: 96487 Sorted by model distance: nonbonded pdb=" OE1 GLN C 473 " pdb=" OG SER C 476 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR B 428 " pdb=" O ALA B 453 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLN D 473 " pdb=" OG SER D 476 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLN A 473 " pdb=" OG SER A 476 " model vdw 2.323 3.040 nonbonded pdb=" OE1 GLN B 473 " pdb=" OG SER B 476 " model vdw 2.324 3.040 ... (remaining 96482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 65 through 198 or (resid 199 through 201 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 239 or (resid 240 a \ nd (name N or name CA or name C or name O or name CB )) or resid 241 through 492 \ or (resid 493 and (name N or name CA or name C or name O or name CB )) or resid \ 494 through 518)) selection = (chain 'B' and (resid 65 through 198 or (resid 199 through 201 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 239 \ or (resid 240 and (name N or name CA or name C or name O or name CB )) or resid \ 241 through 453 or (resid 454 and (name N or name CA or name C or name O or nam \ e CB )) or resid 455 through 462 or (resid 463 and (name N or name CA or name C \ or name O or name CB )) or resid 464 through 518)) selection = (chain 'C' and (resid 65 through 198 or (resid 199 through 201 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 239 \ or (resid 240 and (name N or name CA or name C or name O or name CB )) or resid \ 241 through 462 or (resid 463 and (name N or name CA or name C or name O or nam \ e CB )) or resid 464 through 518)) selection = (chain 'D' and (resid 65 through 199 or (resid 200 through 201 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 462 \ or (resid 463 and (name N or name CA or name C or name O or name CB )) or resid \ 464 through 518)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.360 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.008 0.059 12301 Z= 0.343 Angle : 0.922 8.430 16694 Z= 0.513 Chirality : 0.054 0.178 2014 Planarity : 0.006 0.097 2027 Dihedral : 10.265 79.130 4192 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.62 % Allowed : 3.10 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.18), residues: 1484 helix: -1.22 (0.14), residues: 932 sheet: -2.36 (0.34), residues: 220 loop : -3.35 (0.26), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 395 TYR 0.020 0.002 TYR A 488 PHE 0.023 0.003 PHE A 494 TRP 0.016 0.003 TRP B 480 HIS 0.007 0.002 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00752 (12293) covalent geometry : angle 0.91915 (16678) SS BOND : bond 0.00256 ( 8) SS BOND : angle 2.43948 ( 16) hydrogen bonds : bond 0.15478 ( 917) hydrogen bonds : angle 7.72941 ( 2850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 229 time to evaluate : 0.334 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 346 TRP cc_start: 0.8366 (m100) cc_final: 0.8031 (m-90) REVERT: B 262 LYS cc_start: 0.9146 (mttt) cc_final: 0.8906 (mtpp) REVERT: B 346 TRP cc_start: 0.8393 (m100) cc_final: 0.8031 (m-90) REVERT: C 346 TRP cc_start: 0.8363 (m100) cc_final: 0.8022 (m-90) REVERT: D 346 TRP cc_start: 0.8400 (m100) cc_final: 0.8031 (m-90) outliers start: 8 outliers final: 0 residues processed: 237 average time/residue: 0.1092 time to fit residues: 36.9770 Evaluate side-chains 111 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 137 GLN C 137 GLN D 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.097156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074215 restraints weight = 41637.343| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.46 r_work: 0.3299 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12301 Z= 0.185 Angle : 0.623 10.906 16694 Z= 0.329 Chirality : 0.041 0.147 2014 Planarity : 0.005 0.086 2027 Dihedral : 5.202 39.779 1632 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.16 % Allowed : 8.61 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1484 helix: 0.86 (0.16), residues: 944 sheet: -1.99 (0.31), residues: 248 loop : -2.98 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 212 TYR 0.010 0.001 TYR B 428 PHE 0.013 0.001 PHE D 225 TRP 0.009 0.001 TRP C 390 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00397 (12293) covalent geometry : angle 0.62095 (16678) SS BOND : bond 0.00073 ( 8) SS BOND : angle 1.69427 ( 16) hydrogen bonds : bond 0.04414 ( 917) hydrogen bonds : angle 5.18556 ( 2850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 TRP cc_start: 0.8482 (m100) cc_final: 0.8105 (m-90) REVERT: A 395 ARG cc_start: 0.7591 (tmt90) cc_final: 0.6941 (ttt180) REVERT: B 346 TRP cc_start: 0.8440 (m100) cc_final: 0.8103 (m-90) REVERT: B 395 ARG cc_start: 0.7604 (tmt90) cc_final: 0.6939 (ttt180) REVERT: C 346 TRP cc_start: 0.8473 (m100) cc_final: 0.8094 (m-90) REVERT: C 395 ARG cc_start: 0.7581 (tmt90) cc_final: 0.6927 (ttt180) REVERT: D 346 TRP cc_start: 0.8471 (m100) cc_final: 0.8060 (m-90) REVERT: D 395 ARG cc_start: 0.7590 (tmt90) cc_final: 0.6922 (ttt180) outliers start: 15 outliers final: 9 residues processed: 148 average time/residue: 0.0974 time to fit residues: 21.4222 Evaluate side-chains 119 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.098315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.075556 restraints weight = 42246.196| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.56 r_work: 0.3392 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12301 Z= 0.127 Angle : 0.540 8.365 16694 Z= 0.283 Chirality : 0.039 0.159 2014 Planarity : 0.004 0.070 2027 Dihedral : 4.558 34.383 1632 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.94 % Allowed : 10.32 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1484 helix: 1.63 (0.16), residues: 952 sheet: -1.83 (0.31), residues: 248 loop : -2.64 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 139 TYR 0.007 0.001 TYR B 486 PHE 0.016 0.001 PHE C 210 TRP 0.005 0.001 TRP D 390 HIS 0.006 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00267 (12293) covalent geometry : angle 0.53889 (16678) SS BOND : bond 0.00099 ( 8) SS BOND : angle 1.13023 ( 16) hydrogen bonds : bond 0.04020 ( 917) hydrogen bonds : angle 4.70760 ( 2850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 TRP cc_start: 0.8348 (m100) cc_final: 0.7985 (m-90) REVERT: B 346 TRP cc_start: 0.8325 (m100) cc_final: 0.8009 (m-90) REVERT: B 365 MET cc_start: 0.8382 (ptp) cc_final: 0.8031 (ptp) REVERT: C 346 TRP cc_start: 0.8367 (m100) cc_final: 0.8028 (m-90) REVERT: D 346 TRP cc_start: 0.8363 (m100) cc_final: 0.8003 (m-90) REVERT: D 365 MET cc_start: 0.8382 (ptp) cc_final: 0.8028 (ptp) outliers start: 25 outliers final: 17 residues processed: 162 average time/residue: 0.1007 time to fit residues: 24.4381 Evaluate side-chains 135 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 511 HIS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 511 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 30 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 80 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.097764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.074647 restraints weight = 42154.994| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.53 r_work: 0.3350 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12301 Z= 0.157 Angle : 0.560 9.793 16694 Z= 0.290 Chirality : 0.039 0.150 2014 Planarity : 0.003 0.068 2027 Dihedral : 4.457 30.581 1632 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.64 % Allowed : 10.71 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1484 helix: 1.96 (0.17), residues: 952 sheet: -1.56 (0.33), residues: 228 loop : -2.42 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 139 TYR 0.014 0.001 TYR C 431 PHE 0.012 0.001 PHE A 210 TRP 0.006 0.001 TRP D 390 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00342 (12293) covalent geometry : angle 0.55850 (16678) SS BOND : bond 0.00083 ( 8) SS BOND : angle 1.32695 ( 16) hydrogen bonds : bond 0.03915 ( 917) hydrogen bonds : angle 4.51063 ( 2850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 TRP cc_start: 0.8368 (m100) cc_final: 0.8047 (m-90) REVERT: A 396 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6870 (t80) REVERT: B 346 TRP cc_start: 0.8387 (m100) cc_final: 0.8033 (m-90) REVERT: C 346 TRP cc_start: 0.8399 (m100) cc_final: 0.8056 (m-90) REVERT: C 356 MET cc_start: 0.8064 (mmm) cc_final: 0.7862 (mmt) REVERT: C 396 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6889 (t80) REVERT: D 346 TRP cc_start: 0.8373 (m100) cc_final: 0.8018 (m-90) outliers start: 34 outliers final: 13 residues processed: 169 average time/residue: 0.0986 time to fit residues: 24.7803 Evaluate side-chains 132 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 HIS B 140 HIS C 103 HIS C 140 HIS D 103 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.097195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.074109 restraints weight = 42052.350| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.49 r_work: 0.3454 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12301 Z= 0.175 Angle : 0.583 12.673 16694 Z= 0.297 Chirality : 0.040 0.153 2014 Planarity : 0.003 0.060 2027 Dihedral : 4.401 28.790 1632 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.10 % Allowed : 11.56 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1484 helix: 2.17 (0.16), residues: 944 sheet: -1.62 (0.32), residues: 248 loop : -2.58 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 139 TYR 0.008 0.001 TYR C 431 PHE 0.011 0.001 PHE A 388 TRP 0.005 0.001 TRP A 390 HIS 0.007 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00384 (12293) covalent geometry : angle 0.58137 (16678) SS BOND : bond 0.00127 ( 8) SS BOND : angle 1.38340 ( 16) hydrogen bonds : bond 0.03939 ( 917) hydrogen bonds : angle 4.39840 ( 2850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 TRP cc_start: 0.8341 (m100) cc_final: 0.7970 (m-90) REVERT: A 395 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6828 (tmt90) REVERT: A 396 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6716 (t80) REVERT: B 346 TRP cc_start: 0.8344 (m100) cc_final: 0.7975 (m-90) REVERT: B 396 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6837 (t80) REVERT: C 75 MET cc_start: 0.6050 (ttm) cc_final: 0.5701 (ttt) REVERT: C 346 TRP cc_start: 0.8337 (m100) cc_final: 0.8005 (m-90) REVERT: C 396 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6923 (t80) REVERT: C 471 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8732 (tm-30) REVERT: D 346 TRP cc_start: 0.8319 (m100) cc_final: 0.7963 (m-90) REVERT: D 396 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6853 (t80) outliers start: 40 outliers final: 24 residues processed: 155 average time/residue: 0.0962 time to fit residues: 22.5077 Evaluate side-chains 149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 25 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 125 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.098243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.075629 restraints weight = 42321.259| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.51 r_work: 0.3481 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12301 Z= 0.123 Angle : 0.556 14.728 16694 Z= 0.277 Chirality : 0.038 0.154 2014 Planarity : 0.003 0.056 2027 Dihedral : 4.132 23.680 1632 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.87 % Allowed : 12.65 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.23), residues: 1484 helix: 2.39 (0.16), residues: 944 sheet: -1.35 (0.34), residues: 236 loop : -2.26 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 139 TYR 0.010 0.001 TYR B 486 PHE 0.011 0.001 PHE C 388 TRP 0.005 0.001 TRP A 390 HIS 0.004 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00265 (12293) covalent geometry : angle 0.55536 (16678) SS BOND : bond 0.00064 ( 8) SS BOND : angle 1.19332 ( 16) hydrogen bonds : bond 0.03731 ( 917) hydrogen bonds : angle 4.20804 ( 2850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 TRP cc_start: 0.8343 (m100) cc_final: 0.7970 (m-90) REVERT: A 390 TRP cc_start: 0.8390 (m100) cc_final: 0.7974 (m100) REVERT: A 396 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6832 (t80) REVERT: B 346 TRP cc_start: 0.8326 (m100) cc_final: 0.7995 (m-90) REVERT: B 395 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6792 (tmt90) REVERT: B 396 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6631 (t80) REVERT: C 346 TRP cc_start: 0.8337 (m100) cc_final: 0.8032 (m-90) REVERT: C 390 TRP cc_start: 0.8400 (m100) cc_final: 0.7984 (m100) REVERT: C 395 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6670 (tmt90) REVERT: C 396 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6652 (t80) REVERT: C 471 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8763 (tm-30) REVERT: D 346 TRP cc_start: 0.8334 (m100) cc_final: 0.7989 (m-90) REVERT: D 395 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6793 (tmt90) REVERT: D 396 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6646 (t80) outliers start: 37 outliers final: 22 residues processed: 187 average time/residue: 0.0862 time to fit residues: 24.9124 Evaluate side-chains 163 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.095485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072160 restraints weight = 42177.869| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.49 r_work: 0.3263 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12301 Z= 0.260 Angle : 0.705 14.976 16694 Z= 0.348 Chirality : 0.042 0.164 2014 Planarity : 0.003 0.050 2027 Dihedral : 4.585 23.519 1632 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.18 % Allowed : 14.12 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.22), residues: 1484 helix: 2.08 (0.16), residues: 944 sheet: -1.61 (0.33), residues: 228 loop : -2.39 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 139 TYR 0.008 0.001 TYR C 128 PHE 0.014 0.002 PHE C 494 TRP 0.008 0.001 TRP B 480 HIS 0.004 0.001 HIS D 443 Details of bonding type rmsd covalent geometry : bond 0.00585 (12293) covalent geometry : angle 0.70369 (16678) SS BOND : bond 0.00237 ( 8) SS BOND : angle 1.65625 ( 16) hydrogen bonds : bond 0.04173 ( 917) hydrogen bonds : angle 4.43870 ( 2850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.402 Fit side-chains REVERT: A 346 TRP cc_start: 0.8599 (m100) cc_final: 0.8113 (m-90) REVERT: A 395 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6826 (tmt90) REVERT: A 396 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6765 (t80) REVERT: B 346 TRP cc_start: 0.8640 (m100) cc_final: 0.8074 (m-90) REVERT: B 395 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6902 (tmt90) REVERT: B 396 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6779 (t80) REVERT: C 346 TRP cc_start: 0.8630 (m100) cc_final: 0.8114 (m-90) REVERT: C 395 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6839 (tmt90) REVERT: C 396 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6787 (t80) REVERT: C 471 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8682 (tm-30) REVERT: C 494 PHE cc_start: 0.8706 (m-80) cc_final: 0.8427 (m-80) REVERT: D 346 TRP cc_start: 0.8605 (m100) cc_final: 0.8037 (m-90) REVERT: D 395 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6895 (tmt90) REVERT: D 396 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6753 (t80) outliers start: 41 outliers final: 24 residues processed: 156 average time/residue: 0.0871 time to fit residues: 20.9484 Evaluate side-chains 143 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.097490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.074835 restraints weight = 42235.426| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.52 r_work: 0.3333 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12301 Z= 0.134 Angle : 0.644 16.183 16694 Z= 0.310 Chirality : 0.039 0.167 2014 Planarity : 0.003 0.049 2027 Dihedral : 4.256 20.954 1632 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.72 % Allowed : 15.28 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.23), residues: 1484 helix: 2.31 (0.16), residues: 944 sheet: -1.65 (0.31), residues: 256 loop : -2.34 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 139 TYR 0.010 0.001 TYR A 486 PHE 0.015 0.001 PHE A 494 TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00295 (12293) covalent geometry : angle 0.64287 (16678) SS BOND : bond 0.00101 ( 8) SS BOND : angle 1.15647 ( 16) hydrogen bonds : bond 0.03826 ( 917) hydrogen bonds : angle 4.26569 ( 2850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 346 TRP cc_start: 0.8531 (m100) cc_final: 0.8121 (m-90) REVERT: A 390 TRP cc_start: 0.8501 (m100) cc_final: 0.8047 (m100) REVERT: A 395 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6788 (tmt90) REVERT: A 396 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6621 (t80) REVERT: B 346 TRP cc_start: 0.8532 (m100) cc_final: 0.8117 (m-90) REVERT: B 390 TRP cc_start: 0.8550 (m100) cc_final: 0.8120 (m100) REVERT: B 395 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6910 (tmt90) REVERT: B 396 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6675 (t80) REVERT: C 346 TRP cc_start: 0.8515 (m100) cc_final: 0.8117 (m-90) REVERT: C 390 TRP cc_start: 0.8515 (m100) cc_final: 0.8051 (m100) REVERT: C 395 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6820 (tmt90) REVERT: C 396 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6647 (t80) REVERT: D 161 LEU cc_start: 0.9460 (mt) cc_final: 0.9256 (mt) REVERT: D 346 TRP cc_start: 0.8530 (m100) cc_final: 0.8092 (m-90) REVERT: D 390 TRP cc_start: 0.8549 (m100) cc_final: 0.8123 (m100) REVERT: D 395 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6899 (tmt90) REVERT: D 396 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6643 (t80) outliers start: 35 outliers final: 23 residues processed: 164 average time/residue: 0.0876 time to fit residues: 22.3347 Evaluate side-chains 158 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 33 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.097340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.074420 restraints weight = 42109.267| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.50 r_work: 0.3463 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12301 Z= 0.155 Angle : 0.664 16.336 16694 Z= 0.315 Chirality : 0.040 0.167 2014 Planarity : 0.003 0.046 2027 Dihedral : 4.237 20.776 1632 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.87 % Allowed : 15.05 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.22), residues: 1484 helix: 2.30 (0.16), residues: 944 sheet: -1.67 (0.33), residues: 228 loop : -2.45 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 139 TYR 0.021 0.001 TYR A 117 PHE 0.013 0.001 PHE D 494 TRP 0.009 0.001 TRP D 480 HIS 0.002 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00348 (12293) covalent geometry : angle 0.66312 (16678) SS BOND : bond 0.00142 ( 8) SS BOND : angle 1.27176 ( 16) hydrogen bonds : bond 0.03851 ( 917) hydrogen bonds : angle 4.22312 ( 2850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 346 TRP cc_start: 0.8464 (m100) cc_final: 0.8048 (m-90) REVERT: A 390 TRP cc_start: 0.8333 (m100) cc_final: 0.7908 (m100) REVERT: A 395 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6730 (tmt90) REVERT: A 396 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6681 (t80) REVERT: A 494 PHE cc_start: 0.8670 (m-80) cc_final: 0.8395 (m-80) REVERT: B 346 TRP cc_start: 0.8470 (m100) cc_final: 0.8049 (m-90) REVERT: B 390 TRP cc_start: 0.8350 (m100) cc_final: 0.7930 (m100) REVERT: B 395 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6805 (tmt90) REVERT: B 396 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6654 (t80) REVERT: B 494 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: C 346 TRP cc_start: 0.8437 (m100) cc_final: 0.8022 (m-90) REVERT: C 390 TRP cc_start: 0.8362 (m100) cc_final: 0.7922 (m100) REVERT: C 395 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6718 (tmt90) REVERT: C 396 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6671 (t80) REVERT: C 494 PHE cc_start: 0.8557 (m-80) cc_final: 0.8199 (m-80) REVERT: D 346 TRP cc_start: 0.8477 (m100) cc_final: 0.8026 (m-90) REVERT: D 390 TRP cc_start: 0.8363 (m100) cc_final: 0.7935 (m100) REVERT: D 395 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6802 (tmt90) REVERT: D 396 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6637 (t80) outliers start: 37 outliers final: 25 residues processed: 162 average time/residue: 0.0916 time to fit residues: 22.7996 Evaluate side-chains 160 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 144 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.097704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075145 restraints weight = 42607.635| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.51 r_work: 0.3341 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12301 Z= 0.138 Angle : 0.668 16.359 16694 Z= 0.313 Chirality : 0.040 0.166 2014 Planarity : 0.003 0.044 2027 Dihedral : 4.115 20.176 1632 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.87 % Allowed : 15.21 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.22), residues: 1484 helix: 2.38 (0.16), residues: 944 sheet: -1.61 (0.32), residues: 236 loop : -2.34 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 139 TYR 0.020 0.001 TYR A 117 PHE 0.012 0.001 PHE A 494 TRP 0.008 0.001 TRP D 480 HIS 0.002 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00308 (12293) covalent geometry : angle 0.66694 (16678) SS BOND : bond 0.00125 ( 8) SS BOND : angle 1.17370 ( 16) hydrogen bonds : bond 0.03789 ( 917) hydrogen bonds : angle 4.17400 ( 2850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 346 TRP cc_start: 0.8530 (m100) cc_final: 0.8105 (m-90) REVERT: A 390 TRP cc_start: 0.8485 (m100) cc_final: 0.8057 (m100) REVERT: A 395 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6841 (tmt90) REVERT: A 396 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6693 (t80) REVERT: A 494 PHE cc_start: 0.8773 (m-80) cc_final: 0.8527 (m-80) REVERT: B 346 TRP cc_start: 0.8535 (m100) cc_final: 0.8125 (m-90) REVERT: B 390 TRP cc_start: 0.8522 (m100) cc_final: 0.8089 (m100) REVERT: B 395 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6876 (tmt90) REVERT: B 396 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6715 (t80) REVERT: B 494 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: C 346 TRP cc_start: 0.8536 (m100) cc_final: 0.8109 (m-90) REVERT: C 390 TRP cc_start: 0.8558 (m100) cc_final: 0.8091 (m100) REVERT: C 395 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6797 (tmt90) REVERT: C 396 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6673 (t80) REVERT: C 494 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: D 253 ASP cc_start: 0.8822 (t0) cc_final: 0.8507 (p0) REVERT: D 346 TRP cc_start: 0.8522 (m100) cc_final: 0.8074 (m-90) REVERT: D 390 TRP cc_start: 0.8514 (m100) cc_final: 0.8100 (m100) REVERT: D 395 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6860 (tmt90) REVERT: D 396 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6700 (t80) REVERT: D 494 PHE cc_start: 0.8702 (m-80) cc_final: 0.8381 (m-80) outliers start: 37 outliers final: 27 residues processed: 163 average time/residue: 0.0887 time to fit residues: 22.1189 Evaluate side-chains 162 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 449 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.097831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.075234 restraints weight = 42230.647| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.50 r_work: 0.3355 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12301 Z= 0.135 Angle : 0.664 17.192 16694 Z= 0.311 Chirality : 0.040 0.206 2014 Planarity : 0.003 0.043 2027 Dihedral : 4.089 23.125 1632 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.87 % Allowed : 15.21 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1484 helix: 2.43 (0.16), residues: 944 sheet: -1.64 (0.32), residues: 236 loop : -2.31 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 139 TYR 0.016 0.001 TYR A 117 PHE 0.012 0.001 PHE D 494 TRP 0.008 0.001 TRP B 480 HIS 0.002 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00304 (12293) covalent geometry : angle 0.66302 (16678) SS BOND : bond 0.00129 ( 8) SS BOND : angle 1.15816 ( 16) hydrogen bonds : bond 0.03766 ( 917) hydrogen bonds : angle 4.12012 ( 2850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3052.02 seconds wall clock time: 53 minutes 1.75 seconds (3181.75 seconds total)