Starting phenix.real_space_refine on Wed Oct 28 10:18:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8w_61243/10_2026/9j8w_61243_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8w_61243/10_2026/9j8w_61243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j8w_61243/10_2026/9j8w_61243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8w_61243/10_2026/9j8w_61243.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8w_61243/10_2026/9j8w_61243_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8w_61243/10_2026/9j8w_61243_neut.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 288 5.49 5 S 30 5.16 5 C 8656 2.51 5 N 2821 2.21 5 O 3362 1.98 5 H 12800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27957 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1708 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1434 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1878 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "D" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1559 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1708 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1348 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1878 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "H" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1560 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4611 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 4607 Unusual residues: {'TTD': 1} Classifications: {'DNA': 143, 'undetermined': 1} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 141, None: 2} Not linked: pdbres=" DA J 94 " pdbres="TTD J 95 " Not linked: pdbres="TTD J 95 " pdbres=" DG J 97 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 5666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5666 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 340} Time building chain proxies: 4.56, per 1000 atoms: 0.16 Number of scatterers: 27957 At special positions: 0 Unit cell: (153.7, 128.26, 116.6, 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 30 16.00 P 288 15.00 O 3362 8.00 N 2821 7.00 C 8656 6.00 H 12800 1.00 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: 2.49 Conformation dependent library (CDL) restraints added in 625.4 milliseconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 49.4% alpha, 11.4% beta 130 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.535A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.592A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.801A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.639A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.225A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.861A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 85 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 removed outlier: 3.518A pdb=" N ILE D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 125 removed outlier: 4.157A pdb=" N LYS D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.576A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.516A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.680A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.832A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.665A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.670A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.538A pdb=" N ALA H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 78 removed outlier: 4.206A pdb=" N HIS L 74 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 99 removed outlier: 3.932A pdb=" N ASP L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.377A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.443A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.383A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.282A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'L' and resid 106 through 108 removed outlier: 4.118A pdb=" N LYS L 106 " --> pdb=" O ILE L 417 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE L 417 " --> pdb=" O LYS L 106 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA L 108 " --> pdb=" O ILE L 415 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE L 415 " --> pdb=" O ALA L 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU L 397 " --> pdb=" O ALA L 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 114 through 119 removed outlier: 3.678A pdb=" N SER L 116 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 159 through 164 removed outlier: 3.754A pdb=" N SER L 176 " --> pdb=" O THR L 180 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR L 180 " --> pdb=" O SER L 176 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR L 181 " --> pdb=" O PHE L 194 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE L 190 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 204 through 210 removed outlier: 4.144A pdb=" N SER L 206 " --> pdb=" O GLY L 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 245 through 250 removed outlier: 3.704A pdb=" N SER L 262 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR L 266 " --> pdb=" O SER L 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE L 269 " --> pdb=" O TYR L 283 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR L 283 " --> pdb=" O ILE L 269 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 291 through 296 removed outlier: 3.565A pdb=" N ALA L 293 " --> pdb=" O THR L 306 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL L 314 " --> pdb=" O GLY L 325 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY L 325 " --> pdb=" O VAL L 314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 343 through 344 removed outlier: 6.468A pdb=" N ILE L 372 " --> pdb=" O GLN L 385 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN L 385 " --> pdb=" O ILE L 372 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL L 374 " --> pdb=" O MET L 383 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 626 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12767 1.03 - 1.23: 203 1.23 - 1.42: 6999 1.42 - 1.62: 8820 1.62 - 1.81: 54 Bond restraints: 28843 Sorted by residual: bond pdb=" P TTD J 95 " pdb=" OP2 TTD J 95 " ideal model delta sigma weight residual 1.532 1.708 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" N ILE L 202 " pdb=" H ILE L 202 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" N3T TTD J 95 " pdb=" HT TTD J 95 " ideal model delta sigma weight residual 0.860 1.007 -0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" N3 TTD J 95 " pdb=" HN3 TTD J 95 " ideal model delta sigma weight residual 0.860 1.006 -0.146 2.00e-02 2.50e+03 5.29e+01 bond pdb=" N1 TTD J 95 " pdb=" C2 TTD J 95 " ideal model delta sigma weight residual 1.353 1.492 -0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 28838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.08: 52254 7.08 - 14.15: 13 14.15 - 21.23: 3 21.23 - 28.30: 1 28.30 - 35.38: 3 Bond angle restraints: 52274 Sorted by residual: angle pdb=" CB SER L 68 " pdb=" CA SER L 68 " pdb=" HA SER L 68 " ideal model delta sigma weight residual 109.00 73.62 35.38 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C SER L 68 " pdb=" CA SER L 68 " pdb=" HA SER L 68 " ideal model delta sigma weight residual 109.00 74.26 34.74 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N SER L 68 " pdb=" CA SER L 68 " pdb=" HA SER L 68 " ideal model delta sigma weight residual 110.00 77.65 32.35 3.00e+00 1.11e-01 1.16e+02 angle pdb=" N ASN L 201 " pdb=" CA ASN L 201 " pdb=" C ASN L 201 " ideal model delta sigma weight residual 112.72 101.89 10.83 1.14e+00 7.69e-01 9.03e+01 angle pdb=" OP1 TTD J 95 " pdb=" P TTD J 95 " pdb=" O5' TTD J 95 " ideal model delta sigma weight residual 100.86 122.74 -21.88 3.00e+00 1.11e-01 5.32e+01 ... (remaining 52269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 10717 36.00 - 71.99: 1690 71.99 - 107.99: 60 107.99 - 143.98: 9 143.98 - 179.98: 28 Dihedral angle restraints: 12504 sinusoidal: 8693 harmonic: 3811 Sorted by residual: dihedral pdb=" C THR L 199 " pdb=" N THR L 199 " pdb=" CA THR L 199 " pdb=" CB THR L 199 " ideal model delta harmonic sigma weight residual -122.00 -141.02 19.02 0 2.50e+00 1.60e-01 5.79e+01 dihedral pdb=" N THR L 199 " pdb=" C THR L 199 " pdb=" CA THR L 199 " pdb=" CB THR L 199 " ideal model delta harmonic sigma weight residual 123.40 138.51 -15.11 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" CA LEU B 23 " pdb=" C LEU B 23 " pdb=" N ARG B 24 " pdb=" CA ARG B 24 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 12501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 2506 0.165 - 0.330: 65 0.330 - 0.495: 5 0.495 - 0.660: 0 0.660 - 0.826: 1 Chirality restraints: 2577 Sorted by residual: chirality pdb=" CA THR L 199 " pdb=" N THR L 199 " pdb=" C THR L 199 " pdb=" CB THR L 199 " both_signs ideal model delta sigma weight residual False 2.53 1.70 0.83 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C5 TTD J 95 " pdb=" C4 TTD J 95 " pdb=" C6 TTD J 95 " pdb=" C5T TTD J 95 " both_signs ideal model delta sigma weight residual False -3.16 -2.69 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" P DG J 93 " pdb=" OP1 DG J 93 " pdb=" OP2 DG J 93 " pdb=" O5' DG J 93 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 2574 not shown) Planarity restraints: 3214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 201 " 0.079 2.00e-02 2.50e+03 1.35e-01 1.82e+02 pdb=" N ILE L 202 " -0.233 2.00e-02 2.50e+03 pdb=" CA ILE L 202 " 0.067 2.00e-02 2.50e+03 pdb=" H ILE L 202 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE L 202 " 0.024 2.00e-02 2.50e+03 4.47e-02 1.99e+01 pdb=" N TRP L 203 " -0.077 2.00e-02 2.50e+03 pdb=" CA TRP L 203 " 0.020 2.00e-02 2.50e+03 pdb=" H TRP L 203 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1R TTD J 95 " -0.031 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" C2T TTD J 95 " 0.000 2.00e-02 2.50e+03 pdb=" C4T TTD J 95 " 0.017 2.00e-02 2.50e+03 pdb=" C5T TTD J 95 " -0.056 2.00e-02 2.50e+03 pdb=" C6T TTD J 95 " 0.054 2.00e-02 2.50e+03 pdb=" N1T TTD J 95 " 0.019 2.00e-02 2.50e+03 pdb=" N3T TTD J 95 " 0.000 2.00e-02 2.50e+03 pdb=" O2T TTD J 95 " 0.000 2.00e-02 2.50e+03 pdb=" O4T TTD J 95 " -0.003 2.00e-02 2.50e+03 pdb=" HT TTD J 95 " -0.000 2.00e-02 2.50e+03 ... (remaining 3211 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1442 2.18 - 2.78: 48988 2.78 - 3.39: 74868 3.39 - 3.99: 101727 3.99 - 4.60: 150062 Nonbonded interactions: 377087 Sorted by model distance: nonbonded pdb=" OD2 ASP L 208 " pdb=" H LEU L 250 " model vdw 1.571 2.450 nonbonded pdb=" O HIS L 76 " pdb=" H GLY L 79 " model vdw 1.585 2.450 nonbonded pdb=" OD2 ASP F 69 " pdb="HE22 GLN F 94 " model vdw 1.586 2.450 nonbonded pdb=" OE1 GLU H 106 " pdb=" H GLU H 106 " model vdw 1.621 2.450 nonbonded pdb=" HH TYR B 99 " pdb=" OD2 ASP H 69 " model vdw 1.624 2.450 ... (remaining 377082 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 22 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 23 through 103)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 30 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB o \ r name HG21 or name HG22 or name HG23)) or resid 90 through 126)) } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 94 or resid 96 or resid 9 \ 8 through 145)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 94 or resid 97 through 14 \ 5)) } 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: 3.130 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: 0.050 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.030 Find NCS groups from input model: 0.260 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.007 0.176 16045 Z= 0.568 Angle : 0.890 21.877 22915 Z= 0.688 Chirality : 0.066 0.826 2577 Planarity : 0.005 0.068 1905 Dihedral : 29.242 179.978 6885 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.82 % Allowed : 26.15 % Favored : 73.03 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.26), residues: 1141 helix: 2.19 (0.22), residues: 545 sheet: -0.75 (0.46), residues: 127 loop : -1.43 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 332 TYR 0.023 0.001 TYR D 84 PHE 0.021 0.001 PHE L 149 TRP 0.010 0.001 TRP L 203 HIS 0.011 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.56 (16043) covalent geometry : angle 0.89016 / 0.69 (22915) hydrogen bonds : bond 0.13065 / 8.47 ( 791) hydrogen bonds : angle 4.77753 / 3.29 ( 2024) Misc. bond : bond 0.05696 / 2.99 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 334 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 GLU cc_start: 0.7508 (pt0) cc_final: 0.7304 (pt0) REVERT: L 202 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7876 (mm) REVERT: L 312 ILE cc_start: 0.7890 (mt) cc_final: 0.7645 (mm) outliers start: 8 outliers final: 3 residues processed: 337 average time/residue: 0.4077 time to fit residues: 178.6406 Evaluate side-chains 337 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 333 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain L residue 198 ASP Chi-restraints excluded: chain L residue 202 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN L 349 ASN L 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.144222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122821 restraints weight = 61049.434| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.93 r_work: 0.3480 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.0547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16045 Z= 0.263 Angle : 0.750 9.491 22915 Z= 0.447 Chirality : 0.051 0.365 2577 Planarity : 0.005 0.066 1905 Dihedral : 32.228 179.159 4607 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.63 % Allowed : 24.11 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1141 helix: 2.18 (0.22), residues: 543 sheet: -0.77 (0.45), residues: 128 loop : -1.61 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 93 TYR 0.014 0.002 TYR L 283 PHE 0.014 0.002 PHE E 68 TRP 0.011 0.002 TRP L 203 HIS 0.009 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.26 (16043) covalent geometry : angle 0.75010 / 0.45 (22915) hydrogen bonds : bond 0.06952 / 4.69 ( 791) hydrogen bonds : angle 4.13058 / 2.90 ( 2024) Misc. bond : bond 0.00372 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 350 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 334 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.7700 (mmm) cc_final: 0.7485 (mmm) REVERT: D 96 GLN cc_start: 0.8583 (tp40) cc_final: 0.8163 (tp40) REVERT: F 73 TYR cc_start: 0.8434 (m-80) cc_final: 0.8019 (m-80) REVERT: G 84 LEU cc_start: 0.8392 (mt) cc_final: 0.8149 (mt) REVERT: L 113 ARG cc_start: 0.7178 (ttm-80) cc_final: 0.6850 (ttp-170) REVERT: L 312 ILE cc_start: 0.7878 (mt) cc_final: 0.7624 (mm) outliers start: 16 outliers final: 10 residues processed: 336 average time/residue: 0.4036 time to fit residues: 175.7896 Evaluate side-chains 341 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 331 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain L residue 110 PHE Chi-restraints excluded: chain L residue 191 LEU Chi-restraints excluded: chain L residue 218 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [120, 16, 57, 96, 95, 114, 103, 27, 21, 93, 56] chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN D 85 ASN ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.142694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121109 restraints weight = 60886.013| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.94 r_work: 0.3478 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16045 Z= 0.245 Angle : 0.726 9.658 22915 Z= 0.432 Chirality : 0.049 0.381 2577 Planarity : 0.005 0.068 1905 Dihedral : 32.187 179.340 4602 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.53 % Allowed : 24.11 % Favored : 74.36 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.25), residues: 1141 helix: 2.17 (0.21), residues: 544 sheet: -0.66 (0.47), residues: 123 loop : -1.71 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 332 TYR 0.023 0.002 TYR H 84 PHE 0.013 0.002 PHE E 68 TRP 0.007 0.001 TRP L 203 HIS 0.009 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.24 (16043) covalent geometry : angle 0.72566 / 0.43 (22915) hydrogen bonds : bond 0.06599 / 4.42 ( 791) hydrogen bonds : angle 3.90976 / 2.75 ( 2024) Misc. bond : bond 0.00090 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 332 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 GLU cc_start: 0.7141 (pm20) cc_final: 0.6847 (pm20) REVERT: F 73 TYR cc_start: 0.8467 (m-80) cc_final: 0.8238 (m-80) REVERT: F 78 LYS cc_start: 0.8553 (mmmm) cc_final: 0.8322 (mmtp) REVERT: G 84 LEU cc_start: 0.8346 (mt) cc_final: 0.8068 (mt) REVERT: L 113 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6905 (ttp-110) REVERT: L 285 LEU cc_start: 0.8638 (mp) cc_final: 0.8223 (mp) REVERT: L 332 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7437 (mtm110) outliers start: 15 outliers final: 12 residues processed: 337 average time/residue: 0.4068 time to fit residues: 177.6727 Evaluate side-chains 342 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 330 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 110 PHE Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 283 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [123, 73, 1, 70, 76, 116, 137, 23, 127, 124, 66] chunk 123 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.143343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121823 restraints weight = 60560.162| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.92 r_work: 0.3481 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16045 Z= 0.223 Angle : 0.719 9.649 22915 Z= 0.424 Chirality : 0.049 0.372 2577 Planarity : 0.005 0.068 1905 Dihedral : 32.134 179.892 4598 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.43 % Allowed : 24.41 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1141 helix: 2.21 (0.21), residues: 544 sheet: -0.60 (0.47), residues: 123 loop : -1.72 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 93 TYR 0.020 0.002 TYR D 84 PHE 0.013 0.001 PHE E 68 TRP 0.006 0.001 TRP L 119 HIS 0.006 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.22 (16043) covalent geometry : angle 0.71895 / 0.42 (22915) hydrogen bonds : bond 0.06325 / 4.26 ( 791) hydrogen bonds : angle 3.81211 / 2.68 ( 2024) Misc. bond : bond 0.00092 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 329 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 107 LEU cc_start: 0.8434 (mt) cc_final: 0.8192 (mp) REVERT: E 60 GLU cc_start: 0.7088 (pm20) cc_final: 0.6870 (pm20) REVERT: F 73 TYR cc_start: 0.8447 (m-80) cc_final: 0.8194 (m-80) REVERT: F 78 LYS cc_start: 0.8547 (mmmm) cc_final: 0.8317 (mmtp) REVERT: G 84 LEU cc_start: 0.8343 (mt) cc_final: 0.8060 (mt) REVERT: H 36 GLU cc_start: 0.7732 (pt0) cc_final: 0.7519 (pt0) REVERT: L 113 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6906 (ttp-170) REVERT: L 135 ASP cc_start: 0.6470 (OUTLIER) cc_final: 0.6017 (m-30) REVERT: L 187 LYS cc_start: 0.8507 (mttm) cc_final: 0.8232 (mttm) REVERT: L 285 LEU cc_start: 0.8640 (mp) cc_final: 0.8212 (mp) REVERT: L 332 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7464 (mtm110) outliers start: 14 outliers final: 12 residues processed: 333 average time/residue: 0.3851 time to fit residues: 168.0163 Evaluate side-chains 340 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 327 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain L residue 110 PHE Chi-restraints excluded: chain L residue 135 ASP Chi-restraints excluded: chain L residue 191 LEU Chi-restraints excluded: chain L residue 228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [15, 41, 94, 68, 131, 16, 25, 92, 132, 86, 125] chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.143111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121493 restraints weight = 60718.812| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.93 r_work: 0.3484 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16045 Z= 0.213 Angle : 0.712 9.759 22915 Z= 0.420 Chirality : 0.048 0.377 2577 Planarity : 0.005 0.068 1905 Dihedral : 32.049 179.048 4598 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.74 % Allowed : 24.51 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1141 helix: 2.27 (0.21), residues: 544 sheet: -0.48 (0.47), residues: 120 loop : -1.76 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 93 TYR 0.019 0.002 TYR D 84 PHE 0.012 0.001 PHE E 68 TRP 0.006 0.001 TRP L 320 HIS 0.006 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.21 (16043) covalent geometry : angle 0.71183 / 0.42 (22915) hydrogen bonds : bond 0.06193 / 4.17 ( 791) hydrogen bonds : angle 3.72343 / 2.62 ( 2024) Misc. bond : bond 0.00090 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 328 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 107 LEU cc_start: 0.8440 (mt) cc_final: 0.8198 (mp) REVERT: E 60 GLU cc_start: 0.7121 (pm20) cc_final: 0.6863 (pm20) REVERT: F 73 TYR cc_start: 0.8451 (m-80) cc_final: 0.8161 (m-80) REVERT: F 78 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8335 (mmtp) REVERT: G 84 LEU cc_start: 0.8338 (mt) cc_final: 0.8050 (mt) REVERT: H 36 GLU cc_start: 0.7715 (pt0) cc_final: 0.7474 (pt0) REVERT: L 113 ARG cc_start: 0.7192 (ttm-80) cc_final: 0.6834 (ttp-170) REVERT: L 178 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7921 (mp0) REVERT: L 187 LYS cc_start: 0.8529 (mttm) cc_final: 0.8248 (mttm) REVERT: L 285 LEU cc_start: 0.8650 (mp) cc_final: 0.8221 (mp) REVERT: L 332 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7466 (mtm110) REVERT: L 395 SER cc_start: 0.8027 (m) cc_final: 0.7563 (p) outliers start: 17 outliers final: 13 residues processed: 336 average time/residue: 0.3881 time to fit residues: 170.0492 Evaluate side-chains 340 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 327 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain L residue 110 PHE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 400 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [79, 127, 38, 25, 5, 32, 110, 36, 39, 72, 22] chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.143104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121489 restraints weight = 60673.921| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.92 r_work: 0.3484 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16045 Z= 0.213 Angle : 0.712 10.169 22915 Z= 0.418 Chirality : 0.048 0.372 2577 Planarity : 0.005 0.068 1905 Dihedral : 31.944 178.458 4598 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.63 % Allowed : 24.62 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1141 helix: 2.30 (0.21), residues: 544 sheet: -0.15 (0.50), residues: 109 loop : -1.80 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.016 0.002 TYR D 84 PHE 0.012 0.001 PHE D 66 TRP 0.006 0.001 TRP L 119 HIS 0.005 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.21 (16043) covalent geometry : angle 0.71175 / 0.42 (22915) hydrogen bonds : bond 0.06132 / 4.13 ( 791) hydrogen bonds : angle 3.67344 / 2.59 ( 2024) Misc. bond : bond 0.00085 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 323 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 107 LEU cc_start: 0.8431 (mt) cc_final: 0.8196 (mp) REVERT: E 60 GLU cc_start: 0.7145 (pm20) cc_final: 0.6893 (pm20) REVERT: F 73 TYR cc_start: 0.8448 (m-80) cc_final: 0.8158 (m-80) REVERT: G 84 LEU cc_start: 0.8328 (mt) cc_final: 0.8029 (mt) REVERT: H 36 GLU cc_start: 0.7717 (pt0) cc_final: 0.7461 (pt0) REVERT: L 113 ARG cc_start: 0.7192 (ttm-80) cc_final: 0.6968 (ttp80) REVERT: L 178 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7895 (mp0) REVERT: L 187 LYS cc_start: 0.8531 (mttm) cc_final: 0.8225 (mttm) REVERT: L 285 LEU cc_start: 0.8701 (mp) cc_final: 0.8281 (mp) REVERT: L 386 LEU cc_start: 0.8239 (mm) cc_final: 0.7911 (mp) REVERT: L 395 SER cc_start: 0.8027 (m) cc_final: 0.7566 (p) outliers start: 16 outliers final: 15 residues processed: 330 average time/residue: 0.3841 time to fit residues: 165.8323 Evaluate side-chains 339 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 324 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 110 PHE Chi-restraints excluded: chain L residue 198 ASP Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 400 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [36, 131, 40, 78, 88, 28, 12, 56, 65, 32, 114] chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.142986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121411 restraints weight = 60396.540| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.92 r_work: 0.3484 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16045 Z= 0.214 Angle : 0.709 10.240 22915 Z= 0.417 Chirality : 0.048 0.372 2577 Planarity : 0.005 0.068 1905 Dihedral : 31.858 178.275 4598 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.15 % Allowed : 24.41 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.25), residues: 1141 helix: 2.28 (0.21), residues: 546 sheet: -0.07 (0.50), residues: 108 loop : -1.86 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.019 0.002 TYR D 84 PHE 0.012 0.001 PHE E 68 TRP 0.006 0.001 TRP L 119 HIS 0.006 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.21 (16043) covalent geometry : angle 0.70935 / 0.42 (22915) hydrogen bonds : bond 0.06099 / 4.11 ( 791) hydrogen bonds : angle 3.63416 / 2.55 ( 2024) Misc. bond : bond 0.00071 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 324 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 107 LEU cc_start: 0.8438 (mt) cc_final: 0.8215 (mp) REVERT: E 60 GLU cc_start: 0.7161 (pm20) cc_final: 0.6907 (pm20) REVERT: F 73 TYR cc_start: 0.8451 (m-80) cc_final: 0.8164 (m-80) REVERT: G 84 LEU cc_start: 0.8316 (mt) cc_final: 0.8023 (mt) REVERT: H 36 GLU cc_start: 0.7702 (pt0) cc_final: 0.7463 (pt0) REVERT: L 113 ARG cc_start: 0.7190 (ttm-80) cc_final: 0.6974 (ttp80) REVERT: L 178 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7880 (mp0) REVERT: L 187 LYS cc_start: 0.8510 (mttm) cc_final: 0.8223 (mttm) REVERT: L 285 LEU cc_start: 0.8718 (mp) cc_final: 0.8258 (mp) REVERT: L 386 LEU cc_start: 0.8235 (mm) cc_final: 0.7902 (mp) outliers start: 21 outliers final: 19 residues processed: 334 average time/residue: 0.3987 time to fit residues: 173.9284 Evaluate side-chains 341 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 322 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 110 PHE Chi-restraints excluded: chain L residue 198 ASP Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 400 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [131, 122, 108, 87, 21, 77, 123, 94, 34, 25, 26] chunk 131 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.143214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121602 restraints weight = 60863.484| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.93 r_work: 0.3487 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16045 Z= 0.209 Angle : 0.709 9.880 22915 Z= 0.416 Chirality : 0.048 0.372 2577 Planarity : 0.005 0.068 1905 Dihedral : 31.838 178.335 4598 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.04 % Allowed : 24.62 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1141 helix: 2.28 (0.21), residues: 546 sheet: -0.13 (0.50), residues: 110 loop : -1.87 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 332 TYR 0.033 0.002 TYR D 84 PHE 0.012 0.001 PHE D 66 TRP 0.006 0.001 TRP L 119 HIS 0.005 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.21 (16043) covalent geometry : angle 0.70862 / 0.42 (22915) hydrogen bonds : bond 0.06037 / 4.06 ( 791) hydrogen bonds : angle 3.62239 / 2.54 ( 2024) Misc. bond : bond 0.00077 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 344 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 324 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 107 LEU cc_start: 0.8440 (mt) cc_final: 0.8216 (mp) REVERT: E 60 GLU cc_start: 0.7180 (pm20) cc_final: 0.6917 (pm20) REVERT: F 73 TYR cc_start: 0.8447 (m-80) cc_final: 0.8149 (m-80) REVERT: G 84 LEU cc_start: 0.8304 (mt) cc_final: 0.8010 (mt) REVERT: H 36 GLU cc_start: 0.7720 (pt0) cc_final: 0.7439 (pt0) REVERT: H 46 LEU cc_start: 0.8670 (tp) cc_final: 0.8455 (tt) REVERT: L 113 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6733 (ttp80) REVERT: L 132 LYS cc_start: 0.7305 (ttpt) cc_final: 0.7079 (ttpt) REVERT: L 178 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7877 (mp0) REVERT: L 187 LYS cc_start: 0.8512 (mttm) cc_final: 0.8219 (mttm) REVERT: L 285 LEU cc_start: 0.8724 (mp) cc_final: 0.8257 (mp) REVERT: L 386 LEU cc_start: 0.8235 (mm) cc_final: 0.7905 (mp) outliers start: 20 outliers final: 20 residues processed: 332 average time/residue: 0.3945 time to fit residues: 170.3940 Evaluate side-chains 343 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 323 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 110 PHE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 283 TYR Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 400 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [47, 122, 123, 84, 125, 139, 98, 61, 83, 2, 62] chunk 47 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 139 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.144897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123304 restraints weight = 60895.432| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.92 r_work: 0.3496 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16045 Z= 0.194 Angle : 0.699 9.919 22915 Z= 0.411 Chirality : 0.048 0.372 2577 Planarity : 0.005 0.067 1905 Dihedral : 31.808 178.620 4598 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.74 % Allowed : 24.92 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1141 helix: 2.35 (0.21), residues: 546 sheet: -0.12 (0.50), residues: 110 loop : -1.85 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 332 TYR 0.026 0.002 TYR D 84 PHE 0.012 0.001 PHE D 66 TRP 0.005 0.001 TRP L 119 HIS 0.005 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.19 (16043) covalent geometry : angle 0.69922 / 0.41 (22915) hydrogen bonds : bond 0.05913 / 3.98 ( 791) hydrogen bonds : angle 3.57779 / 2.51 ( 2024) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 320 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 107 LEU cc_start: 0.8436 (mt) cc_final: 0.8088 (mp) REVERT: E 60 GLU cc_start: 0.7158 (pm20) cc_final: 0.6902 (pm20) REVERT: F 73 TYR cc_start: 0.8439 (m-80) cc_final: 0.8135 (m-80) REVERT: G 84 LEU cc_start: 0.8310 (mt) cc_final: 0.8014 (mt) REVERT: H 36 GLU cc_start: 0.7725 (pt0) cc_final: 0.7452 (pt0) REVERT: H 46 LEU cc_start: 0.8674 (tp) cc_final: 0.8458 (tt) REVERT: L 67 ARG cc_start: 0.8177 (tmm-80) cc_final: 0.7868 (tmm-80) REVERT: L 113 ARG cc_start: 0.7207 (ttm-80) cc_final: 0.6755 (ttp80) REVERT: L 132 LYS cc_start: 0.7268 (ttpt) cc_final: 0.7055 (ttpt) REVERT: L 187 LYS cc_start: 0.8482 (mttm) cc_final: 0.8205 (mttm) REVERT: L 285 LEU cc_start: 0.8699 (mp) cc_final: 0.8252 (mp) outliers start: 17 outliers final: 17 residues processed: 328 average time/residue: 0.3910 time to fit residues: 166.1815 Evaluate side-chains 336 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 319 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 110 PHE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 400 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [32, 103, 95, 58, 43, 70, 59, 94, 118, 7, 49] chunk 32 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122357 restraints weight = 60624.256| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.89 r_work: 0.3484 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16045 Z= 0.229 Angle : 0.724 9.783 22915 Z= 0.422 Chirality : 0.049 0.373 2577 Planarity : 0.005 0.070 1905 Dihedral : 31.814 178.274 4598 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.84 % Allowed : 24.82 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1141 helix: 2.27 (0.21), residues: 546 sheet: -0.16 (0.49), residues: 110 loop : -1.87 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.030 0.002 TYR D 84 PHE 0.013 0.002 PHE E 68 TRP 0.010 0.001 TRP L 203 HIS 0.005 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.23 (16043) covalent geometry : angle 0.72415 / 0.42 (22915) hydrogen bonds : bond 0.06153 / 4.14 ( 791) hydrogen bonds : angle 3.62193 / 2.54 ( 2024) Misc. bond : bond 0.00055 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 320 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 107 LEU cc_start: 0.8507 (mt) cc_final: 0.8154 (mp) REVERT: E 60 GLU cc_start: 0.7145 (pm20) cc_final: 0.6901 (pm20) REVERT: F 73 TYR cc_start: 0.8456 (m-80) cc_final: 0.8209 (m-80) REVERT: G 84 LEU cc_start: 0.8347 (mt) cc_final: 0.8057 (mt) REVERT: H 36 GLU cc_start: 0.7718 (pt0) cc_final: 0.7455 (pt0) REVERT: H 46 LEU cc_start: 0.8682 (tp) cc_final: 0.8465 (tt) REVERT: L 67 ARG cc_start: 0.8205 (tmm-80) cc_final: 0.7895 (tmm-80) REVERT: L 113 ARG cc_start: 0.7228 (ttm-80) cc_final: 0.6757 (ttp80) REVERT: L 132 LYS cc_start: 0.7294 (ttpt) cc_final: 0.7093 (ttpt) REVERT: L 285 LEU cc_start: 0.8716 (mp) cc_final: 0.8233 (mp) REVERT: L 386 LEU cc_start: 0.8238 (mm) cc_final: 0.7900 (mp) outliers start: 18 outliers final: 18 residues processed: 328 average time/residue: 0.3884 time to fit residues: 166.3343 Evaluate side-chains 337 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 319 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 110 PHE Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 400 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [125, 85, 9, 0, 69, 15, 128, 72, 8, 96, 79] chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121469 restraints weight = 60913.129| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.90 r_work: 0.3466 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16045 Z= 0.261 Angle : 0.742 9.886 22915 Z= 0.432 Chirality : 0.050 0.372 2577 Planarity : 0.006 0.102 1905 Dihedral : 31.838 177.968 4598 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.74 % Allowed : 25.03 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1141 helix: 2.12 (0.21), residues: 546 sheet: -0.20 (0.49), residues: 110 loop : -1.91 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 332 TYR 0.031 0.002 TYR D 84 PHE 0.015 0.002 PHE E 68 TRP 0.008 0.001 TRP L 119 HIS 0.005 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.26 (16043) covalent geometry : angle 0.74226 / 0.43 (22915) hydrogen bonds : bond 0.06393 / 4.30 ( 791) hydrogen bonds : angle 3.69022 / 2.59 ( 2024) Misc. bond : bond 0.00069 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7719.95 seconds wall clock time: 131 minutes 13.42 seconds (7873.42 seconds total)