Starting phenix.real_space_refine on Wed Jul 30 08:29:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dys_30924/07_2025/7dys_30924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dys_30924/07_2025/7dys_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_30924/07_2025/7dys_30924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dys_30924/07_2025/7dys_30924.map" model { file = "/net/cci-nas-00/data/ceres_data/7dys_30924/07_2025/7dys_30924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dys_30924/07_2025/7dys_30924.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 7.45, per 1000 atoms: 0.62 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: 2.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.20 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: 3.91 Time building geometry restraints manager: 3.25 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: 2.000 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.890 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (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 TRP 0.016 0.003 TRP B 480 HIS 0.007 0.002 HIS D 257 PHE 0.023 0.003 PHE A 494 TYR 0.020 0.002 TYR A 488 ARG 0.010 0.001 ARG D 395 Details of bonding type rmsd hydrogen bonds : bond 0.15478 ( 917) hydrogen bonds : angle 7.72941 ( 2850) SS BOND : bond 0.00256 ( 8) SS BOND : angle 2.43948 ( 16) covalent geometry : bond 0.00752 (12293) covalent geometry : angle 0.91915 (16678) *********************** 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 : 1.909 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: 0.8023 (m-90) REVERT: D 346 TRP cc_start: 0.8401 (m100) cc_final: 0.8031 (m-90) outliers start: 8 outliers final: 0 residues processed: 237 average time/residue: 0.2901 time to fit residues: 97.6352 Evaluate side-chains 116 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 137 GLN B 97 ASN B 137 GLN C 97 ASN C 137 GLN D 97 ASN D 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.098204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075569 restraints weight = 41109.755| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.47 r_work: 0.3333 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2561 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= 0.141 Angle : 0.591 10.661 16694 Z= 0.311 Chirality : 0.039 0.146 2014 Planarity : 0.005 0.085 2027 Dihedral : 4.986 38.611 1632 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.16 % Allowed : 8.46 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1484 helix: 0.90 (0.16), residues: 944 sheet: -1.93 (0.31), residues: 248 loop : -2.93 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 390 HIS 0.002 0.001 HIS D 257 PHE 0.011 0.001 PHE D 225 TYR 0.009 0.001 TYR B 428 ARG 0.004 0.001 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 917) hydrogen bonds : angle 5.09766 ( 2850) SS BOND : bond 0.00114 ( 8) SS BOND : angle 1.46311 ( 16) covalent geometry : bond 0.00294 (12293) covalent geometry : angle 0.59002 (16678) *********************** 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 164 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 TYR cc_start: 0.7432 (p90) cc_final: 0.7130 (p90) REVERT: D 346 TRP cc_start: 0.8418 (m100) cc_final: 0.8021 (m-90) outliers start: 15 outliers final: 10 residues processed: 162 average time/residue: 0.2559 time to fit residues: 61.0761 Evaluate side-chains 117 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 389 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 57 optimal weight: 0.0050 chunk 105 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 220 GLN D 140 HIS D 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.099072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076147 restraints weight = 41442.023| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.56 r_work: 0.3412 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3133 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= 0.122 Angle : 0.541 9.070 16694 Z= 0.281 Chirality : 0.038 0.151 2014 Planarity : 0.004 0.069 2027 Dihedral : 4.523 34.026 1632 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.86 % Allowed : 10.63 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1484 helix: 1.56 (0.17), residues: 952 sheet: -1.76 (0.31), residues: 248 loop : -2.64 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 346 HIS 0.007 0.001 HIS B 443 PHE 0.017 0.001 PHE C 210 TYR 0.020 0.001 TYR A 117 ARG 0.005 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 917) hydrogen bonds : angle 4.68596 ( 2850) SS BOND : bond 0.00034 ( 8) SS BOND : angle 1.19952 ( 16) covalent geometry : bond 0.00252 (12293) covalent geometry : angle 0.53984 (16678) *********************** 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 162 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 TRP cc_start: 0.8438 (m100) cc_final: 0.8154 (m100) REVERT: B 390 TRP cc_start: 0.8509 (m100) cc_final: 0.8217 (m100) REVERT: C 390 TRP cc_start: 0.8474 (m100) cc_final: 0.8193 (m100) REVERT: D 346 TRP cc_start: 0.8333 (m100) cc_final: 0.8005 (m-90) REVERT: D 390 TRP cc_start: 0.8491 (m100) cc_final: 0.8218 (m100) outliers start: 24 outliers final: 13 residues processed: 162 average time/residue: 0.2029 time to fit residues: 49.5280 Evaluate side-chains 134 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 389 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 389 VAL Chi-restraints excluded: chain C residue 148 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 220 GLN B 140 HIS B 220 GLN D 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.097079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.073972 restraints weight = 41798.793| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.52 r_work: 0.3293 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12301 Z= 0.191 Angle : 0.565 5.925 16694 Z= 0.297 Chirality : 0.040 0.154 2014 Planarity : 0.003 0.066 2027 Dihedral : 4.527 30.902 1632 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.78 % Allowed : 12.18 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1484 helix: 1.98 (0.16), residues: 944 sheet: -1.37 (0.35), residues: 208 loop : -2.46 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 346 HIS 0.004 0.001 HIS B 443 PHE 0.012 0.001 PHE D 210 TYR 0.015 0.001 TYR A 117 ARG 0.007 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 917) hydrogen bonds : angle 4.44505 ( 2850) SS BOND : bond 0.00102 ( 8) SS BOND : angle 1.51880 ( 16) covalent geometry : bond 0.00423 (12293) covalent geometry : angle 0.56365 (16678) *********************** 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 148 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 346 TRP cc_start: 0.8444 (m100) cc_final: 0.8086 (m-90) outliers start: 23 outliers final: 12 residues processed: 144 average time/residue: 0.2064 time to fit residues: 45.5536 Evaluate side-chains 123 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 148 THR Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 511 HIS Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 396 TYR 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 128 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS B 103 HIS C 103 HIS D 103 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.096658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073468 restraints weight = 41270.345| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.44 r_work: 0.3443 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12301 Z= 0.181 Angle : 0.589 12.901 16694 Z= 0.300 Chirality : 0.040 0.152 2014 Planarity : 0.003 0.059 2027 Dihedral : 4.429 28.842 1632 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.40 % Allowed : 13.03 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1484 helix: 2.12 (0.16), residues: 944 sheet: -1.52 (0.33), residues: 228 loop : -2.46 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 346 HIS 0.004 0.001 HIS B 443 PHE 0.010 0.001 PHE D 210 TYR 0.013 0.001 TYR B 117 ARG 0.007 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 917) hydrogen bonds : angle 4.38407 ( 2850) SS BOND : bond 0.00140 ( 8) SS BOND : angle 1.44138 ( 16) covalent geometry : bond 0.00401 (12293) covalent geometry : angle 0.58794 (16678) *********************** 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 154 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7520 (tt) REVERT: B 314 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7525 (tt) REVERT: C 139 ARG cc_start: 0.9401 (ttp-170) cc_final: 0.9182 (ttp80) REVERT: C 314 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7506 (tt) REVERT: D 314 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7527 (tt) REVERT: D 346 TRP cc_start: 0.8374 (m100) cc_final: 0.8015 (m-90) REVERT: D 396 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6901 (t80) outliers start: 31 outliers final: 16 residues processed: 150 average time/residue: 0.2696 time to fit residues: 62.3762 Evaluate side-chains 134 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 2.398 ------------------------------------------------------------------------------- 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 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 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 389 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 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 8 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.097197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.073984 restraints weight = 42179.031| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.48 r_work: 0.3449 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12301 Z= 0.158 Angle : 0.573 14.535 16694 Z= 0.289 Chirality : 0.039 0.159 2014 Planarity : 0.003 0.057 2027 Dihedral : 4.325 25.673 1632 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.33 % Allowed : 13.73 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1484 helix: 2.25 (0.16), residues: 944 sheet: -1.50 (0.33), residues: 228 loop : -2.39 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 346 HIS 0.003 0.001 HIS B 443 PHE 0.012 0.001 PHE D 388 TYR 0.012 0.001 TYR B 117 ARG 0.007 0.001 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 917) hydrogen bonds : angle 4.32672 ( 2850) SS BOND : bond 0.00131 ( 8) SS BOND : angle 1.39473 ( 16) covalent geometry : bond 0.00350 (12293) covalent geometry : angle 0.57197 (16678) *********************** 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 156 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 ARG cc_start: 0.9393 (ttp-170) cc_final: 0.9176 (ttp80) REVERT: D 346 TRP cc_start: 0.8388 (m100) cc_final: 0.7981 (m-90) REVERT: D 395 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6743 (tmt90) REVERT: D 396 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6674 (t80) outliers start: 30 outliers final: 16 residues processed: 150 average time/residue: 0.2220 time to fit residues: 50.9549 Evaluate side-chains 134 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 393 VAL 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 393 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 511 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 393 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 395 ARG Chi-restraints excluded: chain D residue 396 TYR 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 10 optimal weight: 0.0980 chunk 148 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.097051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.074158 restraints weight = 42351.318| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.47 r_work: 0.3325 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12301 Z= 0.151 Angle : 0.637 15.451 16694 Z= 0.306 Chirality : 0.040 0.161 2014 Planarity : 0.003 0.051 2027 Dihedral : 4.235 23.055 1632 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.48 % Allowed : 14.43 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1484 helix: 2.25 (0.16), residues: 944 sheet: -1.51 (0.33), residues: 228 loop : -2.38 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 346 HIS 0.003 0.001 HIS B 443 PHE 0.010 0.001 PHE B 494 TYR 0.010 0.001 TYR B 117 ARG 0.006 0.001 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 917) hydrogen bonds : angle 4.32188 ( 2850) SS BOND : bond 0.00125 ( 8) SS BOND : angle 1.32913 ( 16) covalent geometry : bond 0.00335 (12293) covalent geometry : angle 0.63612 (16678) *********************** 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 156 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 346 TRP cc_start: 0.8517 (m100) cc_final: 0.8100 (m-90) REVERT: D 395 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6862 (tmt90) REVERT: D 396 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6620 (t80) outliers start: 32 outliers final: 20 residues processed: 151 average time/residue: 0.2305 time to fit residues: 53.3853 Evaluate side-chains 134 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 389 VAL 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 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 389 VAL Chi-restraints excluded: chain C residue 393 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 30 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.0070 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.0060 overall best weight: 0.4814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 220 GLN C 140 HIS C 220 GLN D 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.098898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.076200 restraints weight = 42686.426| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.56 r_work: 0.3493 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12301 Z= 0.116 Angle : 0.621 16.080 16694 Z= 0.293 Chirality : 0.039 0.163 2014 Planarity : 0.003 0.049 2027 Dihedral : 4.006 19.892 1632 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.02 % Allowed : 15.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.22), residues: 1484 helix: 2.36 (0.16), residues: 944 sheet: -1.48 (0.32), residues: 236 loop : -2.31 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 346 HIS 0.008 0.001 HIS C 140 PHE 0.015 0.001 PHE A 494 TYR 0.014 0.001 TYR D 117 ARG 0.014 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 917) hydrogen bonds : angle 4.21973 ( 2850) SS BOND : bond 0.00091 ( 8) SS BOND : angle 1.15293 ( 16) covalent geometry : bond 0.00249 (12293) covalent geometry : angle 0.62045 (16678) *********************** 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 176 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.8903 (t0) cc_final: 0.8302 (p0) REVERT: A 390 TRP cc_start: 0.8341 (m100) cc_final: 0.7925 (m100) REVERT: B 253 ASP cc_start: 0.8887 (t0) cc_final: 0.8321 (p0) REVERT: B 390 TRP cc_start: 0.8331 (m100) cc_final: 0.7928 (m100) REVERT: C 253 ASP cc_start: 0.8896 (t0) cc_final: 0.8314 (p0) REVERT: C 390 TRP cc_start: 0.8370 (m100) cc_final: 0.7951 (m100) REVERT: D 253 ASP cc_start: 0.8890 (t0) cc_final: 0.8301 (p0) REVERT: D 346 TRP cc_start: 0.8412 (m100) cc_final: 0.8022 (m-90) REVERT: D 390 TRP cc_start: 0.8367 (m100) cc_final: 0.7963 (m100) REVERT: D 395 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6833 (tmt90) REVERT: D 396 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6669 (t80) outliers start: 26 outliers final: 19 residues processed: 171 average time/residue: 0.2038 time to fit residues: 52.8979 Evaluate side-chains 152 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 389 VAL Chi-restraints excluded: chain A residue 393 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 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 389 VAL Chi-restraints excluded: chain C residue 393 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 449 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 220 GLN C 220 GLN D 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.097904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.075322 restraints weight = 42219.706| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.47 r_work: 0.3351 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12301 Z= 0.139 Angle : 0.661 16.632 16694 Z= 0.309 Chirality : 0.039 0.242 2014 Planarity : 0.003 0.045 2027 Dihedral : 3.993 22.455 1632 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.40 % Allowed : 15.75 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1484 helix: 2.37 (0.16), residues: 944 sheet: -1.57 (0.32), residues: 236 loop : -2.23 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 346 HIS 0.003 0.001 HIS C 140 PHE 0.013 0.001 PHE D 494 TYR 0.021 0.001 TYR D 117 ARG 0.011 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 917) hydrogen bonds : angle 4.15134 ( 2850) SS BOND : bond 0.00142 ( 8) SS BOND : angle 1.20274 ( 16) covalent geometry : bond 0.00315 (12293) covalent geometry : angle 0.66071 (16678) *********************** 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 170 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.542 Fit side-chains REVERT: A 253 ASP cc_start: 0.8860 (t0) cc_final: 0.8508 (p0) REVERT: A 390 TRP cc_start: 0.8462 (m100) cc_final: 0.8028 (m100) REVERT: B 253 ASP cc_start: 0.8803 (t0) cc_final: 0.8519 (p0) REVERT: C 253 ASP cc_start: 0.8861 (t0) cc_final: 0.8538 (p0) REVERT: C 390 TRP cc_start: 0.8478 (m100) cc_final: 0.8039 (m100) REVERT: D 253 ASP cc_start: 0.8857 (t0) cc_final: 0.8536 (p0) REVERT: D 346 TRP cc_start: 0.8513 (m100) cc_final: 0.8094 (m-90) REVERT: D 390 TRP cc_start: 0.8498 (m100) cc_final: 0.8092 (m100) REVERT: D 395 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6896 (tmt90) REVERT: D 396 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6664 (t80) REVERT: D 494 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8369 (m-80) outliers start: 31 outliers final: 25 residues processed: 158 average time/residue: 0.1972 time to fit residues: 48.4859 Evaluate side-chains 157 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 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 393 VAL 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 75 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 393 VAL 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 395 ARG Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 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 = 0.3925 r_free = 0.3925 target = 0.097906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.075464 restraints weight = 42094.094| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.44 r_work: 0.3392 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12301 Z= 0.135 Angle : 0.667 17.233 16694 Z= 0.311 Chirality : 0.039 0.272 2014 Planarity : 0.003 0.044 2027 Dihedral : 3.978 22.936 1632 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.33 % Allowed : 15.98 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1484 helix: 2.41 (0.16), residues: 944 sheet: -1.64 (0.32), residues: 236 loop : -2.24 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 346 HIS 0.003 0.001 HIS C 140 PHE 0.013 0.001 PHE A 494 TYR 0.015 0.001 TYR C 117 ARG 0.011 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 917) hydrogen bonds : angle 4.11858 ( 2850) SS BOND : bond 0.00132 ( 8) SS BOND : angle 1.15948 ( 16) covalent geometry : bond 0.00305 (12293) covalent geometry : angle 0.66617 (16678) ********************** 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 164 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.410 Fit side-chains REVERT: A 253 ASP cc_start: 0.8851 (t0) cc_final: 0.8423 (p0) REVERT: A 390 TRP cc_start: 0.8417 (m100) cc_final: 0.7979 (m100) REVERT: A 494 PHE cc_start: 0.8661 (m-80) cc_final: 0.8308 (m-80) REVERT: B 253 ASP cc_start: 0.8829 (t0) cc_final: 0.8451 (p0) REVERT: C 253 ASP cc_start: 0.8870 (t0) cc_final: 0.8452 (p0) REVERT: C 390 TRP cc_start: 0.8443 (m100) cc_final: 0.7996 (m100) REVERT: D 253 ASP cc_start: 0.8856 (t0) cc_final: 0.8450 (p0) REVERT: D 346 TRP cc_start: 0.8485 (m100) cc_final: 0.8103 (m-90) REVERT: D 390 TRP cc_start: 0.8489 (m100) cc_final: 0.8080 (m100) REVERT: D 395 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6874 (tmt90) REVERT: D 396 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6650 (t80) REVERT: D 408 LEU cc_start: 0.9449 (mt) cc_final: 0.9243 (mt) REVERT: D 494 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8215 (m-80) outliers start: 30 outliers final: 23 residues processed: 154 average time/residue: 0.2060 time to fit residues: 49.5835 Evaluate side-chains 154 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 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 417 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 393 VAL 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 395 ARG Chi-restraints excluded: chain D residue 396 TYR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 6 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 12 optimal weight: 0.0050 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.097661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074791 restraints weight = 41999.592| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.47 r_work: 0.3464 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12301 Z= 0.157 Angle : 0.664 16.957 16694 Z= 0.313 Chirality : 0.040 0.244 2014 Planarity : 0.003 0.042 2027 Dihedral : 4.070 20.929 1632 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.33 % Allowed : 16.06 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1484 helix: 2.26 (0.16), residues: 952 sheet: -1.52 (0.33), residues: 208 loop : -2.35 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 346 HIS 0.003 0.001 HIS C 140 PHE 0.012 0.001 PHE C 494 TYR 0.016 0.001 TYR C 117 ARG 0.011 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 917) hydrogen bonds : angle 4.13780 ( 2850) SS BOND : bond 0.00167 ( 8) SS BOND : angle 1.25412 ( 16) covalent geometry : bond 0.00356 (12293) covalent geometry : angle 0.66314 (16678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7275.79 seconds wall clock time: 129 minutes 50.96 seconds (7790.96 seconds total)