Starting phenix.real_space_refine on Wed Jul 30 03:25:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p5a_20254/07_2025/6p5a_20254.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p5a_20254/07_2025/6p5a_20254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p5a_20254/07_2025/6p5a_20254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p5a_20254/07_2025/6p5a_20254.map" model { file = "/net/cci-nas-00/data/ceres_data/6p5a_20254/07_2025/6p5a_20254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p5a_20254/07_2025/6p5a_20254.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 142 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7150 2.51 5 N 2076 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11948 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3568 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 428} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 896 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "G" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3568 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 428} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 980 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "J" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 896 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.22, per 1000 atoms: 0.60 Number of scatterers: 11948 At special positions: 0 Unit cell: (126.44, 110.2, 106.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 142 15.00 Mg 4 11.99 O 2540 8.00 N 2076 7.00 C 7150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 58.7% alpha, 8.2% beta 54 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.673A pdb=" N GLU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 183 removed outlier: 3.790A pdb=" N HIS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.808A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.567A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.558A pdb=" N SER A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.949A pdb=" N ILE A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.820A pdb=" N ALA A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.376A pdb=" N ASP A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 515 Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.974A pdb=" N ASN A 526 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 548 through 563 removed outlier: 3.515A pdb=" N ARG A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 568 removed outlier: 3.792A pdb=" N MET A 567 " --> pdb=" O ASN A 564 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 568 " --> pdb=" O THR A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 564 through 568' Processing helix chain 'B' and resid 620 through 639 Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.711A pdb=" N SER B 657 " --> pdb=" O VAL B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 708 through 734 removed outlier: 3.626A pdb=" N LYS B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 140 removed outlier: 3.673A pdb=" N GLU G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 149 Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'G' and resid 172 through 183 removed outlier: 3.791A pdb=" N HIS G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 197 Processing helix chain 'G' and resid 206 through 213 removed outlier: 3.807A pdb=" N ILE G 210 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET G 213 " --> pdb=" O VAL G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 294 Processing helix chain 'G' and resid 305 through 315 removed outlier: 3.568A pdb=" N LEU G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 354 removed outlier: 3.557A pdb=" N SER G 354 " --> pdb=" O HIS G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 376 Processing helix chain 'G' and resid 387 through 392 removed outlier: 3.950A pdb=" N ILE G 391 " --> pdb=" O ASN G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 408 removed outlier: 3.820A pdb=" N ALA G 404 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 422 Processing helix chain 'G' and resid 428 through 446 Processing helix chain 'G' and resid 465 through 480 removed outlier: 4.377A pdb=" N ASP G 471 " --> pdb=" O ASP G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 491 through 515 Processing helix chain 'G' and resid 521 through 526 removed outlier: 3.974A pdb=" N ASN G 526 " --> pdb=" O SER G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 540 Processing helix chain 'G' and resid 548 through 563 removed outlier: 3.514A pdb=" N ARG G 563 " --> pdb=" O TYR G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 568 removed outlier: 3.792A pdb=" N MET G 567 " --> pdb=" O ASN G 564 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU G 568 " --> pdb=" O THR G 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 564 through 568' Processing helix chain 'H' and resid 620 through 639 Processing helix chain 'H' and resid 652 through 657 removed outlier: 3.711A pdb=" N SER H 657 " --> pdb=" O VAL H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 667 through 682 Processing helix chain 'H' and resid 693 through 702 Processing helix chain 'H' and resid 708 through 734 removed outlier: 3.626A pdb=" N LYS H 712 " --> pdb=" O ASP H 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 205 removed outlier: 6.491A pdb=" N ALA A 257 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 272 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN A 255 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE A 274 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR A 253 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS A 225 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 300 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 227 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER A 302 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 229 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N LEU A 296 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N PHE A 335 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 298 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE A 337 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 300 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.796A pdb=" N ILE A 246 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA4, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.491A pdb=" N ALA G 257 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE G 272 " --> pdb=" O GLN G 255 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN G 255 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE G 274 " --> pdb=" O TYR G 253 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR G 253 " --> pdb=" O PHE G 274 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS G 225 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE G 300 " --> pdb=" O CYS G 225 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU G 227 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER G 302 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE G 229 " --> pdb=" O SER G 302 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N LEU G 296 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N PHE G 335 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL G 298 " --> pdb=" O PHE G 335 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE G 337 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE G 300 " --> pdb=" O PHE G 337 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 239 through 241 removed outlier: 3.795A pdb=" N ILE G 246 " --> pdb=" O ASP G 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 356 through 358 475 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 256 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 3.35 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: 2863 1.34 - 1.45: 3084 1.45 - 1.57: 6177 1.57 - 1.69: 274 1.69 - 1.81: 56 Bond restraints: 12454 Sorted by residual: bond pdb=" C THR A 548 " pdb=" N PRO A 549 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.90e+00 bond pdb=" C THR G 548 " pdb=" N PRO G 549 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.85e+00 bond pdb=" C3' DT E -2 " pdb=" C2' DT E -2 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.08e+00 bond pdb=" C3' DT K -2 " pdb=" C2' DT K -2 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.05e+00 bond pdb=" O5' DA E -3 " pdb=" C5' DA E -3 " ideal model delta sigma weight residual 1.423 1.394 0.029 3.00e-02 1.11e+03 9.50e-01 ... (remaining 12449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 16522 1.09 - 2.19: 692 2.19 - 3.28: 152 3.28 - 4.38: 20 4.38 - 5.47: 12 Bond angle restraints: 17398 Sorted by residual: angle pdb=" C4' DA K -3 " pdb=" C3' DA K -3 " pdb=" C2' DA K -3 " ideal model delta sigma weight residual 102.40 107.10 -4.70 1.50e+00 4.44e-01 9.83e+00 angle pdb=" C4' DA E -3 " pdb=" C3' DA E -3 " pdb=" C2' DA E -3 " ideal model delta sigma weight residual 102.40 107.10 -4.70 1.50e+00 4.44e-01 9.80e+00 angle pdb=" C3' DA K -3 " pdb=" O3' DA K -3 " pdb=" P DT K -2 " ideal model delta sigma weight residual 120.20 116.46 3.74 1.50e+00 4.44e-01 6.21e+00 angle pdb=" C3' DA E -3 " pdb=" O3' DA E -3 " pdb=" P DT E -2 " ideal model delta sigma weight residual 120.20 116.46 3.74 1.50e+00 4.44e-01 6.21e+00 angle pdb=" C4 DT E -13 " pdb=" C5 DT E -13 " pdb=" C7 DT E -13 " ideal model delta sigma weight residual 122.40 118.97 3.43 1.50e+00 4.44e-01 5.23e+00 ... (remaining 17393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.76: 6564 34.76 - 69.51: 518 69.51 - 104.27: 12 104.27 - 139.02: 4 139.02 - 173.78: 6 Dihedral angle restraints: 7104 sinusoidal: 3798 harmonic: 3306 Sorted by residual: dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -31.60 136.20 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C8 GTP G 602 " pdb=" C1' GTP G 602 " pdb=" N9 GTP G 602 " pdb=" O4' GTP G 602 " ideal model delta sinusoidal sigma weight residual 104.59 -31.56 136.16 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C4' DT E -13 " pdb=" C3' DT E -13 " pdb=" O3' DT E -13 " pdb=" P DT E -12 " ideal model delta sinusoidal sigma weight residual -140.00 33.78 -173.78 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1645 0.048 - 0.095: 241 0.095 - 0.143: 55 0.143 - 0.191: 3 0.191 - 0.239: 2 Chirality restraints: 1946 Sorted by residual: chirality pdb=" C3' DA K -3 " pdb=" C4' DA K -3 " pdb=" O3' DA K -3 " pdb=" C2' DA K -3 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' DA E -3 " pdb=" C4' DA E -3 " pdb=" O3' DA E -3 " pdb=" C2' DA E -3 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO G 549 " pdb=" N PRO G 549 " pdb=" C PRO G 549 " pdb=" CB PRO G 549 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1943 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN G 268 " -0.034 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO G 269 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 269 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 269 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 268 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 269 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 172 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO G 173 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " 0.023 5.00e-02 4.00e+02 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 30 2.49 - 3.09: 7784 3.09 - 3.70: 18319 3.70 - 4.30: 27816 4.30 - 4.90: 43456 Nonbonded interactions: 97405 Sorted by model distance: nonbonded pdb=" OD1 ASN A 440 " pdb="MG MG A 602 " model vdw 1.890 2.170 nonbonded pdb=" OD1 ASN G 440 " pdb="MG MG G 603 " model vdw 1.907 2.170 nonbonded pdb=" O3' DA I 9 " pdb="MG MG G 601 " model vdw 2.077 2.170 nonbonded pdb=" O3' DA C 9 " pdb="MG MG A 603 " model vdw 2.078 2.170 nonbonded pdb=" OD2 ASP A 303 " pdb="MG MG A 603 " model vdw 2.135 2.170 ... (remaining 97400 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 128 through 569 or resid 603)) selection = (chain 'G' and (resid 128 through 569 or resid 603)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 31.250 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 0.587 12456 Z= 0.753 Angle : 0.526 5.475 17398 Z= 0.316 Chirality : 0.037 0.239 1946 Planarity : 0.004 0.052 1730 Dihedral : 20.140 173.780 4960 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.69 (0.22), residues: 1112 helix: -0.46 (0.18), residues: 622 sheet: -2.11 (0.47), residues: 60 loop : -1.85 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 442 HIS 0.002 0.001 HIS G 546 PHE 0.014 0.001 PHE A 272 TYR 0.008 0.001 TYR H 629 ARG 0.002 0.000 ARG G 569 Details of bonding type rmsd hydrogen bonds : bond 0.14780 ( 613) hydrogen bonds : angle 5.33899 ( 1645) covalent geometry : bond 0.00263 (12454) covalent geometry : angle 0.52604 (17398) Misc. bond : bond 0.58555 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.178 Fit side-chains REVERT: A 273 ASP cc_start: 0.7712 (t70) cc_final: 0.7429 (t0) REVERT: A 476 MET cc_start: 0.8352 (tpp) cc_final: 0.7614 (tpt) REVERT: A 563 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.6931 (ptm160) REVERT: A 567 MET cc_start: 0.7410 (tpp) cc_final: 0.7168 (tpt) REVERT: B 700 LEU cc_start: 0.8528 (tt) cc_final: 0.7511 (mt) REVERT: G 239 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7741 (mm-30) REVERT: G 273 ASP cc_start: 0.7731 (t70) cc_final: 0.7445 (t0) REVERT: G 476 MET cc_start: 0.8359 (tpp) cc_final: 0.7617 (tpt) REVERT: G 563 ARG cc_start: 0.7332 (ptm-80) cc_final: 0.6935 (ptm160) REVERT: G 567 MET cc_start: 0.7427 (tpp) cc_final: 0.7150 (tpt) REVERT: H 700 LEU cc_start: 0.8525 (tt) cc_final: 0.7504 (mt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2992 time to fit residues: 92.8343 Evaluate side-chains 134 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 546 HIS B 669 GLN B 685 ASN B 686 ASN G 150 ASN G 546 HIS H 669 GLN H 685 ASN H 686 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110813 restraints weight = 15083.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114230 restraints weight = 9406.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116610 restraints weight = 6875.105| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12456 Z= 0.210 Angle : 0.572 7.241 17398 Z= 0.321 Chirality : 0.039 0.153 1946 Planarity : 0.004 0.052 1730 Dihedral : 25.117 174.054 2698 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.39 % Allowed : 9.82 % Favored : 88.79 % 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: -0.29 (0.24), residues: 1112 helix: 0.67 (0.19), residues: 616 sheet: -1.09 (0.51), residues: 72 loop : -1.24 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 312 HIS 0.004 0.001 HIS G 342 PHE 0.012 0.001 PHE A 493 TYR 0.016 0.001 TYR A 559 ARG 0.004 0.001 ARG A 563 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 613) hydrogen bonds : angle 3.84798 ( 1645) covalent geometry : bond 0.00482 (12454) covalent geometry : angle 0.57202 (17398) Misc. bond : bond 0.00296 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.129 Fit side-chains REVERT: A 370 GLU cc_start: 0.7606 (tt0) cc_final: 0.7405 (tt0) REVERT: A 476 MET cc_start: 0.8570 (tpp) cc_final: 0.7881 (tpt) REVERT: A 563 ARG cc_start: 0.7319 (ptm-80) cc_final: 0.6972 (ptp90) REVERT: A 567 MET cc_start: 0.7418 (tpp) cc_final: 0.7183 (tpt) REVERT: B 674 GLU cc_start: 0.7818 (tp30) cc_final: 0.7534 (tp30) REVERT: B 696 GLU cc_start: 0.8097 (tp30) cc_final: 0.7891 (tm-30) REVERT: G 370 GLU cc_start: 0.7611 (tt0) cc_final: 0.7395 (tt0) REVERT: G 476 MET cc_start: 0.8575 (tpp) cc_final: 0.7864 (tpt) REVERT: G 563 ARG cc_start: 0.7314 (ptm-80) cc_final: 0.6938 (ptp90) REVERT: G 567 MET cc_start: 0.7453 (tpp) cc_final: 0.7196 (tpt) REVERT: H 674 GLU cc_start: 0.7816 (tp30) cc_final: 0.7214 (tp30) REVERT: H 696 GLU cc_start: 0.8084 (tp30) cc_final: 0.7812 (tm-30) outliers start: 14 outliers final: 5 residues processed: 153 average time/residue: 0.2426 time to fit residues: 53.2276 Evaluate side-chains 124 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 415 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 546 HIS G 308 ASN G 546 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112056 restraints weight = 15179.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115588 restraints weight = 9382.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118021 restraints weight = 6790.683| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12456 Z= 0.166 Angle : 0.525 7.072 17398 Z= 0.292 Chirality : 0.037 0.132 1946 Planarity : 0.004 0.055 1730 Dihedral : 24.720 175.504 2698 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.19 % Allowed : 11.90 % Favored : 86.90 % 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: 0.42 (0.25), residues: 1112 helix: 1.33 (0.20), residues: 616 sheet: -0.63 (0.55), residues: 72 loop : -1.13 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 312 HIS 0.003 0.001 HIS A 342 PHE 0.010 0.001 PHE A 324 TYR 0.018 0.001 TYR G 559 ARG 0.003 0.000 ARG H 719 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 613) hydrogen bonds : angle 3.58667 ( 1645) covalent geometry : bond 0.00377 (12454) covalent geometry : angle 0.52480 (17398) Misc. bond : bond 0.00203 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.200 Fit side-chains REVERT: A 395 SER cc_start: 0.7907 (m) cc_final: 0.7575 (t) REVERT: A 476 MET cc_start: 0.8531 (tpp) cc_final: 0.7884 (tpt) REVERT: A 563 ARG cc_start: 0.7410 (ptm-80) cc_final: 0.6924 (ptp90) REVERT: A 567 MET cc_start: 0.7430 (tpp) cc_final: 0.7193 (tpt) REVERT: B 696 GLU cc_start: 0.7956 (tp30) cc_final: 0.7747 (tm-30) REVERT: G 239 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7650 (mm-30) REVERT: G 395 SER cc_start: 0.7911 (m) cc_final: 0.7570 (t) REVERT: G 476 MET cc_start: 0.8529 (tpp) cc_final: 0.7863 (tpt) REVERT: G 563 ARG cc_start: 0.7430 (ptm-80) cc_final: 0.6910 (ptp90) outliers start: 12 outliers final: 3 residues processed: 125 average time/residue: 0.2294 time to fit residues: 42.9022 Evaluate side-chains 111 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain G residue 415 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 102 optimal weight: 0.0030 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 7 optimal weight: 0.3980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 684 ASN H 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115596 restraints weight = 14965.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119361 restraints weight = 9048.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121950 restraints weight = 6457.063| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12456 Z= 0.131 Angle : 0.499 7.020 17398 Z= 0.278 Chirality : 0.036 0.131 1946 Planarity : 0.003 0.051 1730 Dihedral : 24.553 176.179 2698 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.89 % Allowed : 13.19 % Favored : 85.91 % 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: 0.98 (0.25), residues: 1112 helix: 1.71 (0.21), residues: 618 sheet: -0.12 (0.67), residues: 48 loop : -0.77 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 312 HIS 0.003 0.000 HIS A 342 PHE 0.008 0.001 PHE A 493 TYR 0.021 0.001 TYR A 559 ARG 0.002 0.000 ARG G 555 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 613) hydrogen bonds : angle 3.43718 ( 1645) covalent geometry : bond 0.00287 (12454) covalent geometry : angle 0.49890 (17398) Misc. bond : bond 0.00138 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.077 Fit side-chains REVERT: A 303 ASP cc_start: 0.8325 (t0) cc_final: 0.7543 (t0) REVERT: A 370 GLU cc_start: 0.7543 (tt0) cc_final: 0.7295 (tt0) REVERT: A 476 MET cc_start: 0.8457 (tpp) cc_final: 0.7836 (tpt) REVERT: A 563 ARG cc_start: 0.7364 (ptm-80) cc_final: 0.6763 (ptp90) REVERT: G 370 GLU cc_start: 0.7541 (tt0) cc_final: 0.7292 (tt0) REVERT: G 476 MET cc_start: 0.8439 (tpp) cc_final: 0.7851 (tpt) REVERT: G 563 ARG cc_start: 0.7386 (ptm-80) cc_final: 0.6807 (ptp90) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.2552 time to fit residues: 48.8141 Evaluate side-chains 122 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain H residue 680 LEU Chi-restraints excluded: chain H residue 700 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.141064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113237 restraints weight = 15013.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116683 restraints weight = 9428.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119052 restraints weight = 6887.773| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12456 Z= 0.156 Angle : 0.526 6.842 17398 Z= 0.289 Chirality : 0.037 0.127 1946 Planarity : 0.003 0.044 1730 Dihedral : 24.685 174.943 2698 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.99 % Allowed : 14.58 % Favored : 84.42 % 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: 1.08 (0.25), residues: 1112 helix: 1.72 (0.21), residues: 622 sheet: -0.19 (0.60), residues: 62 loop : -0.61 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 312 HIS 0.003 0.001 HIS A 342 PHE 0.011 0.001 PHE A 493 TYR 0.021 0.001 TYR A 559 ARG 0.004 0.000 ARG A 540 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 613) hydrogen bonds : angle 3.46906 ( 1645) covalent geometry : bond 0.00352 (12454) covalent geometry : angle 0.52592 (17398) Misc. bond : bond 0.00150 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.175 Fit side-chains REVERT: A 303 ASP cc_start: 0.8390 (t0) cc_final: 0.7608 (t0) REVERT: A 370 GLU cc_start: 0.7792 (tt0) cc_final: 0.7520 (tt0) REVERT: A 395 SER cc_start: 0.8039 (m) cc_final: 0.7673 (t) REVERT: A 476 MET cc_start: 0.8534 (tpp) cc_final: 0.7867 (tpt) REVERT: A 563 ARG cc_start: 0.7394 (ptm-80) cc_final: 0.6947 (ptp90) REVERT: G 370 GLU cc_start: 0.7767 (tt0) cc_final: 0.7495 (tt0) REVERT: G 395 SER cc_start: 0.8093 (m) cc_final: 0.7720 (t) REVERT: G 476 MET cc_start: 0.8530 (tpp) cc_final: 0.7844 (tpt) REVERT: G 563 ARG cc_start: 0.7414 (ptm-80) cc_final: 0.6838 (ptp90) outliers start: 10 outliers final: 5 residues processed: 126 average time/residue: 0.2672 time to fit residues: 48.4340 Evaluate side-chains 119 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 655 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 685 ASN H 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113850 restraints weight = 15149.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117387 restraints weight = 9395.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119839 restraints weight = 6815.505| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12456 Z= 0.150 Angle : 0.519 6.858 17398 Z= 0.285 Chirality : 0.036 0.142 1946 Planarity : 0.003 0.043 1730 Dihedral : 24.660 175.801 2698 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.89 % Allowed : 14.88 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1112 helix: 1.85 (0.21), residues: 622 sheet: 0.37 (0.61), residues: 58 loop : -0.62 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 312 HIS 0.003 0.001 HIS A 342 PHE 0.011 0.001 PHE A 493 TYR 0.018 0.001 TYR G 559 ARG 0.005 0.000 ARG A 540 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 613) hydrogen bonds : angle 3.40211 ( 1645) covalent geometry : bond 0.00338 (12454) covalent geometry : angle 0.51909 (17398) Misc. bond : bond 0.00145 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.071 Fit side-chains REVERT: A 303 ASP cc_start: 0.8496 (t0) cc_final: 0.7689 (t0) REVERT: A 370 GLU cc_start: 0.7728 (tt0) cc_final: 0.7378 (tt0) REVERT: A 395 SER cc_start: 0.8153 (m) cc_final: 0.7761 (t) REVERT: A 476 MET cc_start: 0.8526 (tpp) cc_final: 0.7867 (tpt) REVERT: A 563 ARG cc_start: 0.7539 (ptm-80) cc_final: 0.7063 (ptp90) REVERT: G 370 GLU cc_start: 0.7735 (tt0) cc_final: 0.7375 (tt0) REVERT: G 395 SER cc_start: 0.8168 (m) cc_final: 0.7778 (t) REVERT: G 476 MET cc_start: 0.8531 (tpp) cc_final: 0.7895 (tpt) REVERT: G 563 ARG cc_start: 0.7553 (ptm-80) cc_final: 0.7035 (ptp90) outliers start: 9 outliers final: 9 residues processed: 125 average time/residue: 0.2598 time to fit residues: 46.1380 Evaluate side-chains 125 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 329 ASP Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 655 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.142026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.114091 restraints weight = 15054.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117678 restraints weight = 9369.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120131 restraints weight = 6785.164| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12456 Z= 0.135 Angle : 0.513 7.022 17398 Z= 0.280 Chirality : 0.036 0.137 1946 Planarity : 0.003 0.040 1730 Dihedral : 24.588 176.147 2698 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.29 % Allowed : 15.38 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1112 helix: 1.90 (0.20), residues: 626 sheet: 0.53 (0.60), residues: 58 loop : -0.59 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 312 HIS 0.002 0.000 HIS A 342 PHE 0.010 0.001 PHE A 493 TYR 0.016 0.001 TYR G 559 ARG 0.007 0.000 ARG A 540 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 613) hydrogen bonds : angle 3.34336 ( 1645) covalent geometry : bond 0.00300 (12454) covalent geometry : angle 0.51329 (17398) Misc. bond : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.063 Fit side-chains REVERT: A 370 GLU cc_start: 0.7743 (tt0) cc_final: 0.7372 (tt0) REVERT: A 395 SER cc_start: 0.8066 (m) cc_final: 0.7680 (t) REVERT: A 456 ILE cc_start: 0.5868 (OUTLIER) cc_final: 0.5604 (mp) REVERT: A 476 MET cc_start: 0.8503 (tpp) cc_final: 0.7875 (tpt) REVERT: A 563 ARG cc_start: 0.7391 (ptm-80) cc_final: 0.6956 (ptp90) REVERT: G 370 GLU cc_start: 0.7750 (tt0) cc_final: 0.7372 (tt0) REVERT: G 395 SER cc_start: 0.8129 (m) cc_final: 0.7730 (t) REVERT: G 456 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5620 (mp) REVERT: G 476 MET cc_start: 0.8443 (tpp) cc_final: 0.7820 (tpt) REVERT: G 478 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7558 (tt0) REVERT: G 563 ARG cc_start: 0.7421 (ptm-80) cc_final: 0.6941 (ptp90) outliers start: 13 outliers final: 6 residues processed: 130 average time/residue: 0.2662 time to fit residues: 49.3358 Evaluate side-chains 125 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain H residue 655 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 102 optimal weight: 0.0670 chunk 75 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.143517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115295 restraints weight = 15126.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119008 restraints weight = 9319.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121506 restraints weight = 6707.245| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12456 Z= 0.145 Angle : 0.520 7.231 17398 Z= 0.283 Chirality : 0.036 0.137 1946 Planarity : 0.003 0.041 1730 Dihedral : 24.627 175.760 2698 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.39 % Allowed : 15.38 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1112 helix: 1.95 (0.21), residues: 624 sheet: 0.46 (0.60), residues: 68 loop : -0.46 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 312 HIS 0.002 0.000 HIS A 342 PHE 0.010 0.001 PHE A 493 TYR 0.016 0.001 TYR A 559 ARG 0.006 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 613) hydrogen bonds : angle 3.37227 ( 1645) covalent geometry : bond 0.00326 (12454) covalent geometry : angle 0.51987 (17398) Misc. bond : bond 0.00141 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.138 Fit side-chains REVERT: A 303 ASP cc_start: 0.8502 (t0) cc_final: 0.7690 (t0) REVERT: A 370 GLU cc_start: 0.7713 (tt0) cc_final: 0.7355 (tt0) REVERT: A 395 SER cc_start: 0.8130 (m) cc_final: 0.7774 (t) REVERT: A 456 ILE cc_start: 0.5789 (OUTLIER) cc_final: 0.5528 (mp) REVERT: A 476 MET cc_start: 0.8508 (tpp) cc_final: 0.7856 (tpt) REVERT: A 563 ARG cc_start: 0.7440 (ptm-80) cc_final: 0.7003 (ptp90) REVERT: G 303 ASP cc_start: 0.8420 (t0) cc_final: 0.7572 (t0) REVERT: G 370 GLU cc_start: 0.7720 (tt0) cc_final: 0.7353 (tt0) REVERT: G 395 SER cc_start: 0.8151 (m) cc_final: 0.7801 (t) REVERT: G 456 ILE cc_start: 0.5803 (OUTLIER) cc_final: 0.5540 (mp) REVERT: G 476 MET cc_start: 0.8508 (tpp) cc_final: 0.7840 (tpt) REVERT: G 478 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7584 (tt0) REVERT: G 563 ARG cc_start: 0.7471 (ptm-80) cc_final: 0.6989 (ptp90) outliers start: 14 outliers final: 10 residues processed: 121 average time/residue: 0.2369 time to fit residues: 42.3872 Evaluate side-chains 124 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain H residue 655 GLU Chi-restraints excluded: chain H residue 700 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.0570 chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.144187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116086 restraints weight = 14965.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119773 restraints weight = 9213.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122342 restraints weight = 6640.973| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12456 Z= 0.138 Angle : 0.514 7.627 17398 Z= 0.279 Chirality : 0.036 0.138 1946 Planarity : 0.003 0.039 1730 Dihedral : 24.606 176.018 2698 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.59 % Allowed : 15.18 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1112 helix: 1.96 (0.20), residues: 622 sheet: 0.60 (0.60), residues: 68 loop : -0.46 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 312 HIS 0.002 0.000 HIS A 342 PHE 0.010 0.001 PHE A 493 TYR 0.015 0.001 TYR G 559 ARG 0.004 0.000 ARG G 540 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 613) hydrogen bonds : angle 3.37290 ( 1645) covalent geometry : bond 0.00309 (12454) covalent geometry : angle 0.51364 (17398) Misc. bond : bond 0.00135 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.7706 (tt0) cc_final: 0.7373 (tt0) REVERT: A 395 SER cc_start: 0.8125 (m) cc_final: 0.7760 (t) REVERT: A 456 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5697 (mp) REVERT: A 476 MET cc_start: 0.8526 (tpp) cc_final: 0.7906 (tpt) REVERT: A 563 ARG cc_start: 0.7428 (ptm-80) cc_final: 0.7001 (ptp90) REVERT: G 303 ASP cc_start: 0.8408 (t0) cc_final: 0.7558 (t0) REVERT: G 370 GLU cc_start: 0.7709 (tt0) cc_final: 0.7370 (tt0) REVERT: G 395 SER cc_start: 0.8149 (m) cc_final: 0.7788 (t) REVERT: G 456 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5713 (mp) REVERT: G 476 MET cc_start: 0.8500 (tpp) cc_final: 0.7868 (tpt) REVERT: G 478 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7561 (tt0) REVERT: G 563 ARG cc_start: 0.7461 (ptm-80) cc_final: 0.6993 (ptp90) REVERT: H 619 MET cc_start: 0.7820 (mtp) cc_final: 0.7588 (mtm) outliers start: 16 outliers final: 9 residues processed: 120 average time/residue: 0.2255 time to fit residues: 40.5403 Evaluate side-chains 120 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain H residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.143202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115104 restraints weight = 14967.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118781 restraints weight = 9257.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121298 restraints weight = 6673.857| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12456 Z= 0.152 Angle : 0.531 7.732 17398 Z= 0.286 Chirality : 0.036 0.135 1946 Planarity : 0.003 0.039 1730 Dihedral : 24.674 175.610 2698 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.09 % Allowed : 15.08 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1112 helix: 1.94 (0.21), residues: 622 sheet: 0.70 (0.60), residues: 68 loop : -0.43 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 312 HIS 0.003 0.001 HIS A 342 PHE 0.011 0.001 PHE A 493 TYR 0.015 0.001 TYR G 559 ARG 0.004 0.000 ARG A 540 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 613) hydrogen bonds : angle 3.40311 ( 1645) covalent geometry : bond 0.00343 (12454) covalent geometry : angle 0.53125 (17398) Misc. bond : bond 0.00143 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.238 Fit side-chains REVERT: A 303 ASP cc_start: 0.8530 (t0) cc_final: 0.7693 (t0) REVERT: A 370 GLU cc_start: 0.7792 (tt0) cc_final: 0.7412 (tt0) REVERT: A 456 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5702 (mp) REVERT: A 476 MET cc_start: 0.8536 (tpp) cc_final: 0.7930 (tpt) REVERT: A 563 ARG cc_start: 0.7441 (ptm-80) cc_final: 0.7002 (ptp90) REVERT: G 303 ASP cc_start: 0.8428 (t0) cc_final: 0.7573 (t0) REVERT: G 370 GLU cc_start: 0.7791 (tt0) cc_final: 0.7418 (tt0) REVERT: G 395 SER cc_start: 0.8200 (m) cc_final: 0.7818 (t) REVERT: G 456 ILE cc_start: 0.5958 (OUTLIER) cc_final: 0.5718 (mp) REVERT: G 476 MET cc_start: 0.8512 (tpp) cc_final: 0.7852 (tpt) REVERT: G 478 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7540 (tt0) REVERT: G 563 ARG cc_start: 0.7464 (ptm-80) cc_final: 0.6991 (ptp90) outliers start: 11 outliers final: 9 residues processed: 117 average time/residue: 0.2264 time to fit residues: 39.3200 Evaluate side-chains 120 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain H residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.143887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116101 restraints weight = 14915.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119688 restraints weight = 9351.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122146 restraints weight = 6795.668| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12456 Z= 0.143 Angle : 0.525 7.732 17398 Z= 0.284 Chirality : 0.036 0.138 1946 Planarity : 0.003 0.039 1730 Dihedral : 24.630 176.013 2698 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.29 % Allowed : 15.08 % Favored : 83.63 % 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: 1.50 (0.25), residues: 1112 helix: 1.96 (0.20), residues: 622 sheet: 0.76 (0.61), residues: 68 loop : -0.40 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 312 HIS 0.002 0.000 HIS A 342 PHE 0.010 0.001 PHE A 493 TYR 0.015 0.001 TYR G 559 ARG 0.004 0.000 ARG G 540 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 613) hydrogen bonds : angle 3.38138 ( 1645) covalent geometry : bond 0.00321 (12454) covalent geometry : angle 0.52490 (17398) Misc. bond : bond 0.00139 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.01 seconds wall clock time: 60 minutes 17.58 seconds (3617.58 seconds total)