Starting phenix.real_space_refine on Thu Jul 2 03:33:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vcl_64957/07_2026/9vcl_64957.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vcl_64957/07_2026/9vcl_64957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vcl_64957/07_2026/9vcl_64957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vcl_64957/07_2026/9vcl_64957.map" model { file = "/net/cci-nas-00/data/ceres_data/9vcl_64957/07_2026/9vcl_64957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vcl_64957/07_2026/9vcl_64957.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 5 6.06 5 P 55 5.49 5 S 52 5.16 5 C 3743 2.51 5 N 1056 2.21 5 O 1306 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6220 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4089 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 26, 'TRANS': 485} Chain breaks: 1 Chain: "P" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'RNA': 26} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 14} Link IDs: {'rna3p': 25} Chain: "T" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 596 Classifications: {'RNA': 28} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 13} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 3 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'EIF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 37.113 23.394 44.080 1.00 41.73 S ATOM 546 SG CYS A 77 40.727 24.949 43.307 1.00 43.10 S ATOM 651 SG CYS A 90 39.528 22.020 41.919 1.00 53.02 S ATOM 2581 SG CYS B 207 33.917 21.184 76.044 1.00 40.24 S ATOM 2601 SG CYS B 210 31.737 21.485 79.938 1.00 50.80 S ATOM 2722 SG CYS B 226 35.695 23.025 78.375 1.00 33.31 S ATOM 3022 SG CYS B 261 53.283 51.455 82.167 1.00 60.41 S ATOM 3152 SG CYS B 279 50.229 49.907 79.979 1.00 33.40 S ATOM 4542 SG CYS B 452 30.429 34.066 127.830 1.00124.04 S ATOM 4698 SG CYS B 484 31.964 32.968 125.423 1.00132.93 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N EIF P 101 " occ=0.97 ... (22 atoms not shown) pdb=" P EIF P 101 " occ=0.97 Time building chain proxies: 1.39, per 1000 atoms: 0.22 Number of scatterers: 6220 At special positions: 0 Unit cell: (77.38, 99.28, 139.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 Ca 2 19.99 S 52 16.00 P 55 15.00 F 1 9.00 O 1306 8.00 N 1056 7.00 C 3743 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 379.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 207 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 210 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 279 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 261 " pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 452 " pdb="ZN ZN B 605 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 484 " Number of angles added : 8 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1202 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 26.9% alpha, 13.8% beta 23 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.537A pdb=" N ASP A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 4.119A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 106 through 114 removed outlier: 4.028A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.793A pdb=" N MET B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.693A pdb=" N VAL B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 3.678A pdb=" N THR B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 194' Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.699A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.677A pdb=" N ASP B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.666A pdb=" N ALA B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B 283 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 removed outlier: 3.507A pdb=" N VAL B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.807A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'B' and resid 487 through 505 Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.952A pdb=" N ASN B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.534A pdb=" N THR B 35 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 38 " --> pdb=" O THR B 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.741A pdb=" N VAL B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 111 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.741A pdb=" N VAL B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 111 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 89 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE B 183 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.664A pdb=" N SER B 134 " --> pdb=" O GLY B 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.711A pdb=" N GLU B 364 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE B 350 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B 329 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR B 351 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP B 331 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 381 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 397 through 401 Processing sheet with id=AA8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'B' and resid 446 through 447 removed outlier: 6.328A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 111 hydrogen bonds defined for protein. 300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 875 1.30 - 1.43: 2143 1.43 - 1.56: 3287 1.56 - 1.68: 111 1.68 - 1.81: 68 Bond restraints: 6484 Sorted by residual: bond pdb=" C2 EIF P 101 " pdb=" C3 EIF P 101 " ideal model delta sigma weight residual 1.542 1.312 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3 EIF P 101 " pdb=" O5 EIF P 101 " ideal model delta sigma weight residual 1.462 1.652 -0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" CA ASP B 273 " pdb=" C ASP B 273 " ideal model delta sigma weight residual 1.524 1.421 0.103 1.24e-02 6.50e+03 6.90e+01 bond pdb=" CA ALA B 274 " pdb=" CB ALA B 274 " ideal model delta sigma weight residual 1.537 1.425 0.112 1.38e-02 5.25e+03 6.61e+01 bond pdb=" CA ALA A 71 " pdb=" C ALA A 71 " ideal model delta sigma weight residual 1.524 1.423 0.101 1.29e-02 6.01e+03 6.12e+01 ... (remaining 6479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.36: 9035 7.36 - 14.73: 22 14.73 - 22.09: 7 22.09 - 29.46: 1 29.46 - 36.82: 1 Bond angle restraints: 9066 Sorted by residual: angle pdb=" N GLY B 265 " pdb=" CA GLY B 265 " pdb=" C GLY B 265 " ideal model delta sigma weight residual 113.18 150.00 -36.82 2.37e+00 1.78e-01 2.41e+02 angle pdb=" N ASN B 266 " pdb=" CA ASN B 266 " pdb=" C ASN B 266 " ideal model delta sigma weight residual 107.75 83.67 24.08 1.86e+00 2.89e-01 1.68e+02 angle pdb=" C ARG B 76 " pdb=" CA ARG B 76 " pdb=" CB ARG B 76 " ideal model delta sigma weight residual 110.68 131.17 -20.49 1.70e+00 3.46e-01 1.45e+02 angle pdb=" N ASP B 273 " pdb=" CA ASP B 273 " pdb=" C ASP B 273 " ideal model delta sigma weight residual 113.19 95.38 17.81 1.58e+00 4.01e-01 1.27e+02 angle pdb=" N ASN B 238 " pdb=" CA ASN B 238 " pdb=" C ASN B 238 " ideal model delta sigma weight residual 108.12 87.62 20.50 1.97e+00 2.58e-01 1.08e+02 ... (remaining 9061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3324 17.92 - 35.83: 364 35.83 - 53.75: 111 53.75 - 71.67: 61 71.67 - 89.58: 9 Dihedral angle restraints: 3869 sinusoidal: 1997 harmonic: 1872 Sorted by residual: dihedral pdb=" C VAL B 287 " pdb=" N VAL B 287 " pdb=" CA VAL B 287 " pdb=" CB VAL B 287 " ideal model delta harmonic sigma weight residual -122.00 -149.34 27.34 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" C ARG B 76 " pdb=" N ARG B 76 " pdb=" CA ARG B 76 " pdb=" CB ARG B 76 " ideal model delta harmonic sigma weight residual -122.60 -148.76 26.16 0 2.50e+00 1.60e-01 1.09e+02 dihedral pdb=" N ASN B 266 " pdb=" C ASN B 266 " pdb=" CA ASN B 266 " pdb=" CB ASN B 266 " ideal model delta harmonic sigma weight residual 122.80 97.03 25.77 0 2.50e+00 1.60e-01 1.06e+02 ... (remaining 3866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 1033 0.226 - 0.452: 3 0.452 - 0.678: 3 0.678 - 0.904: 1 0.904 - 1.130: 3 Chirality restraints: 1043 Sorted by residual: chirality pdb=" CA TYR B 237 " pdb=" N TYR B 237 " pdb=" C TYR B 237 " pdb=" CB TYR B 237 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CA ARG B 76 " pdb=" N ARG B 76 " pdb=" C ARG B 76 " pdb=" CB ARG B 76 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA VAL B 287 " pdb=" N VAL B 287 " pdb=" C VAL B 287 " pdb=" CB VAL B 287 " both_signs ideal model delta sigma weight residual False 2.44 1.45 0.99 2.00e-01 2.50e+01 2.43e+01 ... (remaining 1040 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 68 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.66e+00 pdb=" C PHE A 68 " -0.054 2.00e-02 2.50e+03 pdb=" O PHE A 68 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY A 69 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 19 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO B 20 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 20 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 20 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 120 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO B 121 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " 0.029 5.00e-02 4.00e+02 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 40 2.44 - 3.06: 4150 3.06 - 3.67: 9941 3.67 - 4.29: 14666 4.29 - 4.90: 22880 Nonbonded interactions: 51677 Sorted by model distance: nonbonded pdb=" OD2 ASP B 90 " pdb="CA CA B 601 " model vdw 1.826 3.250 nonbonded pdb=" OE2 GLU B 92 " pdb="CA CA B 601 " model vdw 1.844 3.250 nonbonded pdb=" OD2 ASP B 273 " pdb="CA CA B 601 " model vdw 1.921 3.250 nonbonded pdb=" O LYS B 200 " pdb=" O TYR B 237 " model vdw 1.948 3.040 nonbonded pdb=" OG1 THR B 127 " pdb=" O ASN B 130 " model vdw 2.148 3.040 ... (remaining 51672 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.97 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: 5.820 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.014 0.529 6500 Z= 0.725 Angle : 1.308 36.822 9074 Z= 0.717 Chirality : 0.084 1.130 1043 Planarity : 0.005 0.055 959 Dihedral : 17.658 89.582 2667 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.99 % Allowed : 13.00 % Favored : 85.02 % Cbeta Deviations : 1.83 % 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: -4.52 (0.27), residues: 637 helix: -3.23 (0.33), residues: 141 sheet: -3.89 (0.56), residues: 57 loop : -2.99 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 213 TYR 0.020 0.002 TYR B 69 PHE 0.035 0.003 PHE B 190 TRP 0.015 0.002 TRP B 159 HIS 0.005 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.01201 / 0.64 ( 6484) covalent geometry : angle 1.24091 / 0.71 ( 9066) hydrogen bonds : bond 0.29700 / 19.47 ( 153) hydrogen bonds : angle 9.48386 / 6.39 ( 380) metal coordination : bond 0.15815 / 8.05 ( 15) metal coordination : angle 13.99856 / 6.90 ( 8) Misc. bond : bond 0.15399 / 8.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7625 (mt0) REVERT: A 103 CYS cc_start: 0.8161 (m) cc_final: 0.7937 (m) REVERT: B 352 ASP cc_start: 0.6838 (m-30) cc_final: 0.6369 (p0) outliers start: 11 outliers final: 2 residues processed: 128 average time/residue: 0.1018 time to fit residues: 16.1966 Evaluate side-chains 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 288 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 40 ASN A 53 GLN A 98 GLN A 114 ASN B 22 GLN B 67 ASN B 95 HIS B 108 GLN B 116 ASN B 188 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 486 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.143072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.091737 restraints weight = 10364.476| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.65 r_work: 0.2994 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 6500 Z= 0.303 Angle : 0.752 10.632 9074 Z= 0.390 Chirality : 0.046 0.209 1043 Planarity : 0.005 0.053 959 Dihedral : 16.668 73.538 1525 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.15 % Allowed : 16.97 % Favored : 78.88 % 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: -3.66 (0.28), residues: 637 helix: -2.49 (0.36), residues: 147 sheet: -2.50 (0.65), residues: 55 loop : -2.55 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 98 TYR 0.015 0.002 TYR B 447 PHE 0.024 0.002 PHE B 146 TRP 0.018 0.002 TRP B 159 HIS 0.007 0.002 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.30 ( 6484) covalent geometry : angle 0.73273 / 0.39 ( 9066) hydrogen bonds : bond 0.09521 / 5.08 ( 153) hydrogen bonds : angle 5.49801 / 3.76 ( 380) metal coordination : bond 0.02980 / 1.51 ( 15) metal coordination : angle 5.73245 / 2.97 ( 8) Misc. bond : bond 0.00872 / 0.46 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.9311 (tptp) cc_final: 0.9098 (tptt) REVERT: A 89 PHE cc_start: 0.8534 (m-10) cc_final: 0.8249 (m-80) REVERT: A 106 ASP cc_start: 0.8171 (p0) cc_final: 0.7723 (p0) REVERT: B 302 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7171 (mp0) REVERT: B 352 ASP cc_start: 0.7070 (m-30) cc_final: 0.6027 (p0) outliers start: 23 outliers final: 12 residues processed: 94 average time/residue: 0.0659 time to fit residues: 8.3801 Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.0470 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.144800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.094854 restraints weight = 10203.672| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.60 r_work: 0.3056 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 6500 Z= 0.135 Angle : 0.595 10.550 9074 Z= 0.309 Chirality : 0.040 0.152 1043 Planarity : 0.004 0.044 959 Dihedral : 16.401 73.638 1519 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.61 % Allowed : 18.05 % Favored : 78.34 % 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: -3.06 (0.30), residues: 637 helix: -1.89 (0.39), residues: 145 sheet: -2.20 (0.71), residues: 55 loop : -2.19 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 212 TYR 0.014 0.001 TYR B 491 PHE 0.011 0.001 PHE A 16 TRP 0.010 0.002 TRP B 159 HIS 0.011 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 6484) covalent geometry : angle 0.58495 / 0.31 ( 9066) hydrogen bonds : bond 0.09573 / 4.95 ( 153) hydrogen bonds : angle 5.00921 / 3.42 ( 380) metal coordination : bond 0.01316 / 0.60 ( 15) metal coordination : angle 3.65026 / 2.01 ( 8) Misc. bond : bond 0.00141 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.9250 (tptp) cc_final: 0.9045 (tptt) REVERT: A 40 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8199 (t0) REVERT: A 89 PHE cc_start: 0.8584 (m-10) cc_final: 0.8352 (m-80) REVERT: A 106 ASP cc_start: 0.8039 (p0) cc_final: 0.7623 (p0) REVERT: B 61 LYS cc_start: 0.8324 (mttm) cc_final: 0.8100 (mmtp) REVERT: B 155 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8192 (ptpt) REVERT: B 302 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7212 (mp0) REVERT: B 351 TYR cc_start: 0.7840 (m-80) cc_final: 0.7347 (m-10) REVERT: B 352 ASP cc_start: 0.7120 (m-30) cc_final: 0.6085 (p0) outliers start: 20 outliers final: 11 residues processed: 86 average time/residue: 0.0702 time to fit residues: 8.2212 Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 0.0040 chunk 60 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 188 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 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 = 0.4098 r_free = 0.4098 target = 0.145184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.091420 restraints weight = 10301.108| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.37 r_work: 0.3089 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6500 Z= 0.138 Angle : 0.558 9.831 9074 Z= 0.288 Chirality : 0.039 0.151 1043 Planarity : 0.004 0.040 959 Dihedral : 16.022 73.730 1519 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.25 % Allowed : 18.77 % Favored : 77.98 % 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: -2.66 (0.31), residues: 637 helix: -1.43 (0.42), residues: 142 sheet: -2.39 (0.73), residues: 49 loop : -1.91 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 98 TYR 0.014 0.001 TYR B 491 PHE 0.013 0.001 PHE A 19 TRP 0.008 0.001 TRP B 186 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6484) covalent geometry : angle 0.55160 / 0.29 ( 9066) hydrogen bonds : bond 0.09093 / 4.64 ( 153) hydrogen bonds : angle 4.70453 / 3.21 ( 380) metal coordination : bond 0.01391 / 0.71 ( 15) metal coordination : angle 2.89912 / 1.59 ( 8) Misc. bond : bond 0.00150 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.9299 (tptp) cc_final: 0.9076 (tptt) REVERT: A 40 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8101 (t0) REVERT: A 106 ASP cc_start: 0.8160 (p0) cc_final: 0.7741 (p0) REVERT: B 38 LEU cc_start: 0.8468 (mp) cc_final: 0.8260 (mt) REVERT: B 61 LYS cc_start: 0.8493 (mttm) cc_final: 0.8235 (mmtp) REVERT: B 302 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7417 (mp0) REVERT: B 351 TYR cc_start: 0.7936 (m-80) cc_final: 0.7512 (m-10) outliers start: 18 outliers final: 14 residues processed: 81 average time/residue: 0.0691 time to fit residues: 7.4953 Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.145392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.094894 restraints weight = 10551.564| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.81 r_work: 0.3039 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6500 Z= 0.120 Angle : 0.534 9.633 9074 Z= 0.276 Chirality : 0.039 0.173 1043 Planarity : 0.004 0.041 959 Dihedral : 15.808 73.703 1519 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.43 % Allowed : 19.68 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.31), residues: 637 helix: -1.17 (0.43), residues: 142 sheet: -2.38 (0.75), residues: 44 loop : -1.81 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 98 TYR 0.014 0.001 TYR B 491 PHE 0.012 0.001 PHE A 19 TRP 0.009 0.001 TRP B 186 HIS 0.007 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6484) covalent geometry : angle 0.52978 / 0.28 ( 9066) hydrogen bonds : bond 0.08879 / 4.51 ( 153) hydrogen bonds : angle 4.55434 / 3.11 ( 380) metal coordination : bond 0.01166 / 0.60 ( 15) metal coordination : angle 2.32730 / 1.27 ( 8) Misc. bond : bond 0.00090 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.177 Fit side-chains REVERT: A 25 LYS cc_start: 0.9219 (tptp) cc_final: 0.8989 (tptt) REVERT: A 40 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8032 (t0) REVERT: A 66 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8201 (mt-10) REVERT: A 106 ASP cc_start: 0.7916 (p0) cc_final: 0.7582 (p0) REVERT: B 38 LEU cc_start: 0.8454 (mp) cc_final: 0.8192 (mt) REVERT: B 61 LYS cc_start: 0.8400 (mttm) cc_final: 0.8152 (mmtp) REVERT: B 302 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7464 (mp0) REVERT: B 315 MET cc_start: 0.8538 (tpp) cc_final: 0.8022 (tpp) REVERT: B 351 TYR cc_start: 0.7901 (m-80) cc_final: 0.7411 (m-10) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.0624 time to fit residues: 7.1337 Evaluate side-chains 83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 9 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 229 HIS ** 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 = 0.4098 r_free = 0.4098 target = 0.145307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.094978 restraints weight = 10286.313| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.63 r_work: 0.3070 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6500 Z= 0.107 Angle : 0.527 10.287 9074 Z= 0.268 Chirality : 0.039 0.147 1043 Planarity : 0.004 0.039 959 Dihedral : 15.643 73.689 1519 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.43 % Allowed : 19.68 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.32), residues: 637 helix: -0.99 (0.43), residues: 142 sheet: -2.55 (0.73), residues: 49 loop : -1.66 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 98 TYR 0.015 0.001 TYR B 491 PHE 0.013 0.001 PHE B 444 TRP 0.008 0.001 TRP B 186 HIS 0.007 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6484) covalent geometry : angle 0.52391 / 0.27 ( 9066) hydrogen bonds : bond 0.08737 / 4.43 ( 153) hydrogen bonds : angle 4.46863 / 3.05 ( 380) metal coordination : bond 0.00868 / 0.45 ( 15) metal coordination : angle 1.94535 / 1.07 ( 8) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.198 Fit side-chains REVERT: A 25 LYS cc_start: 0.9207 (tptp) cc_final: 0.8983 (tptt) REVERT: A 106 ASP cc_start: 0.7820 (p0) cc_final: 0.7514 (p0) REVERT: B 61 LYS cc_start: 0.8376 (mttm) cc_final: 0.8166 (mmtp) REVERT: B 315 MET cc_start: 0.8555 (tpp) cc_final: 0.8099 (tpp) REVERT: B 351 TYR cc_start: 0.7950 (m-80) cc_final: 0.7438 (m-10) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.0599 time to fit residues: 7.1274 Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 66 optimal weight: 8.9990 chunk 30 optimal weight: 0.0770 chunk 67 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.146257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094804 restraints weight = 10311.338| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.61 r_work: 0.3078 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6500 Z= 0.106 Angle : 0.523 10.025 9074 Z= 0.269 Chirality : 0.039 0.146 1043 Planarity : 0.004 0.041 959 Dihedral : 15.434 73.553 1519 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.07 % Allowed : 20.40 % Favored : 76.53 % 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: -2.11 (0.32), residues: 637 helix: -0.73 (0.44), residues: 136 sheet: -2.48 (0.70), residues: 52 loop : -1.56 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 98 TYR 0.017 0.001 TYR B 491 PHE 0.016 0.001 PHE B 444 TRP 0.013 0.001 TRP B 348 HIS 0.007 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 6484) covalent geometry : angle 0.52036 / 0.27 ( 9066) hydrogen bonds : bond 0.08560 / 4.34 ( 153) hydrogen bonds : angle 4.39545 / 3.01 ( 380) metal coordination : bond 0.00766 / 0.41 ( 15) metal coordination : angle 1.71221 / 0.93 ( 8) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.128 Fit side-chains REVERT: A 25 LYS cc_start: 0.9187 (tptp) cc_final: 0.8947 (tptt) REVERT: A 28 LYS cc_start: 0.8675 (tmtt) cc_final: 0.8178 (mtmm) REVERT: A 106 ASP cc_start: 0.7714 (p0) cc_final: 0.7421 (p0) REVERT: B 315 MET cc_start: 0.8541 (tpp) cc_final: 0.8150 (tpp) REVERT: B 326 PHE cc_start: 0.8483 (m-80) cc_final: 0.8247 (m-80) REVERT: B 351 TYR cc_start: 0.7944 (m-80) cc_final: 0.7490 (m-80) outliers start: 17 outliers final: 12 residues processed: 81 average time/residue: 0.0588 time to fit residues: 6.3683 Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 40.0000 chunk 56 optimal weight: 0.9980 chunk 52 optimal weight: 0.0030 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.145514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094934 restraints weight = 10293.109| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.56 r_work: 0.3072 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6500 Z= 0.117 Angle : 0.529 10.277 9074 Z= 0.266 Chirality : 0.039 0.147 1043 Planarity : 0.004 0.045 959 Dihedral : 15.342 73.718 1519 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.89 % Allowed : 19.68 % Favored : 77.44 % 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: -1.97 (0.32), residues: 637 helix: -0.65 (0.44), residues: 139 sheet: -2.30 (0.71), residues: 52 loop : -1.46 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 98 TYR 0.015 0.001 TYR B 491 PHE 0.015 0.001 PHE B 444 TRP 0.008 0.001 TRP B 186 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 6484) covalent geometry : angle 0.52584 / 0.27 ( 9066) hydrogen bonds : bond 0.08362 / 4.27 ( 153) hydrogen bonds : angle 4.32089 / 2.96 ( 380) metal coordination : bond 0.00913 / 0.52 ( 15) metal coordination : angle 1.88260 / 1.00 ( 8) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.159 Fit side-chains REVERT: A 28 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8247 (mtmm) REVERT: A 40 ASN cc_start: 0.8726 (t0) cc_final: 0.8358 (t0) REVERT: A 106 ASP cc_start: 0.7661 (p0) cc_final: 0.7425 (p0) REVERT: B 315 MET cc_start: 0.8556 (tpp) cc_final: 0.8199 (tpp) REVERT: B 326 PHE cc_start: 0.8490 (m-80) cc_final: 0.8260 (m-80) REVERT: B 351 TYR cc_start: 0.8030 (m-80) cc_final: 0.7435 (m-80) REVERT: B 352 ASP cc_start: 0.7072 (m-30) cc_final: 0.5838 (p0) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 0.0666 time to fit residues: 7.2159 Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.0000 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 47 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.144842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092058 restraints weight = 10170.103| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.53 r_work: 0.3065 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6500 Z= 0.114 Angle : 0.547 13.939 9074 Z= 0.279 Chirality : 0.039 0.251 1043 Planarity : 0.004 0.058 959 Dihedral : 15.252 73.541 1519 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.53 % Allowed : 20.04 % Favored : 77.44 % 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: -1.85 (0.32), residues: 637 helix: -0.52 (0.45), residues: 139 sheet: -2.31 (0.69), residues: 52 loop : -1.39 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 98 TYR 0.015 0.001 TYR B 491 PHE 0.014 0.001 PHE B 444 TRP 0.009 0.001 TRP B 348 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 6484) covalent geometry : angle 0.54464 / 0.28 ( 9066) hydrogen bonds : bond 0.08224 / 4.19 ( 153) hydrogen bonds : angle 4.28209 / 2.94 ( 380) metal coordination : bond 0.00872 / 0.50 ( 15) metal coordination : angle 1.74420 / 0.90 ( 8) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.178 Fit side-chains REVERT: A 28 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8182 (mtmm) REVERT: A 40 ASN cc_start: 0.8713 (t0) cc_final: 0.8319 (t0) REVERT: B 315 MET cc_start: 0.8520 (tpp) cc_final: 0.8162 (tpp) REVERT: B 326 PHE cc_start: 0.8540 (m-80) cc_final: 0.8314 (m-80) REVERT: B 351 TYR cc_start: 0.7980 (m-80) cc_final: 0.7359 (m-80) REVERT: B 352 ASP cc_start: 0.6966 (m-30) cc_final: 0.5714 (p0) outliers start: 14 outliers final: 13 residues processed: 76 average time/residue: 0.0656 time to fit residues: 6.8228 Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 0.0000 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.144491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088732 restraints weight = 10070.775| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.32 r_work: 0.3084 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6500 Z= 0.126 Angle : 0.549 10.179 9074 Z= 0.278 Chirality : 0.039 0.222 1043 Planarity : 0.004 0.048 959 Dihedral : 15.171 73.655 1519 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.53 % Allowed : 19.86 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.32), residues: 637 helix: -0.43 (0.45), residues: 139 sheet: -2.19 (0.68), residues: 52 loop : -1.34 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 98 TYR 0.014 0.001 TYR B 498 PHE 0.018 0.001 PHE B 444 TRP 0.009 0.001 TRP B 186 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6484) covalent geometry : angle 0.54688 / 0.28 ( 9066) hydrogen bonds : bond 0.08089 / 4.14 ( 153) hydrogen bonds : angle 4.29152 / 2.96 ( 380) metal coordination : bond 0.01022 / 0.59 ( 15) metal coordination : angle 1.63217 / 0.85 ( 8) Misc. bond : bond 0.00027 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.161 Fit side-chains REVERT: A 28 LYS cc_start: 0.8789 (tmtt) cc_final: 0.8296 (mtmm) REVERT: A 40 ASN cc_start: 0.8799 (t0) cc_final: 0.8396 (t0) REVERT: B 315 MET cc_start: 0.8589 (tpp) cc_final: 0.8244 (tpp) REVERT: B 351 TYR cc_start: 0.8102 (m-80) cc_final: 0.7495 (m-80) REVERT: B 352 ASP cc_start: 0.7129 (m-30) cc_final: 0.5849 (p0) outliers start: 14 outliers final: 12 residues processed: 77 average time/residue: 0.0571 time to fit residues: 6.0056 Evaluate side-chains 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 40.0000 chunk 27 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 49 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.144136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091074 restraints weight = 10083.079| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.27 r_work: 0.3075 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6500 Z= 0.131 Angle : 0.547 11.055 9074 Z= 0.275 Chirality : 0.039 0.194 1043 Planarity : 0.004 0.048 959 Dihedral : 15.117 73.677 1519 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.71 % Allowed : 19.86 % Favored : 77.44 % 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: -1.73 (0.32), residues: 637 helix: -0.36 (0.45), residues: 139 sheet: -2.07 (0.68), residues: 52 loop : -1.35 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 98 TYR 0.016 0.001 TYR B 368 PHE 0.015 0.001 PHE B 444 TRP 0.010 0.001 TRP B 186 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6484) covalent geometry : angle 0.54448 / 0.27 ( 9066) hydrogen bonds : bond 0.07968 / 4.09 ( 153) hydrogen bonds : angle 4.31143 / 2.97 ( 380) metal coordination : bond 0.01077 / 0.61 ( 15) metal coordination : angle 1.77364 / 0.84 ( 8) Misc. bond : bond 0.00038 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.97 seconds wall clock time: 34 minutes 15.41 seconds (2055.41 seconds total)