Starting phenix.real_space_refine on Thu Jul 2 02:38:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrl_73370/07_2026/9yrl_73370.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrl_73370/07_2026/9yrl_73370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yrl_73370/07_2026/9yrl_73370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrl_73370/07_2026/9yrl_73370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yrl_73370/07_2026/9yrl_73370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrl_73370/07_2026/9yrl_73370.map" } resolution = 2.9 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= 0.011 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 Zn 5 6.06 5 P 35 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 3561 2.51 5 N 989 2.21 5 O 1164 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 8 residue(s): 0.01s 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: 5808 Number of models: 1 Model: "" Number of chains: 7 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: 4086 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 511, 4076 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 26, 'TRANS': 484} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 511, 4076 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 26, 'TRANS': 484} Chain breaks: 1 bond proxies already assigned to first conformer: 4182 Chain: "C" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 680 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 16, 'rna3p_pyr': 14} Link IDs: {'rna2p': 2, 'rna3p': 29} Chain breaks: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 2} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 50.778 76.370 70.055 1.00 53.46 S ATOM 546 SG CYS A 77 50.123 74.396 73.283 1.00 45.86 S ATOM 651 SG CYS A 90 51.965 77.703 73.424 1.00 58.85 S ATOM 854 SG CYS A 117 54.768 96.439 67.492 1.00 99.85 S ATOM 874 SG CYS A 120 51.666 97.623 69.149 1.00 94.16 S ATOM 935 SG CYS A 128 52.007 97.793 65.359 1.00111.32 S ATOM 947 SG CYS A 130 53.808 100.292 67.524 1.00120.94 S ATOM 2578 SG CYS B 207 68.642 60.320 48.534 1.00 51.68 S ATOM 2598 SG CYS B 210 69.646 59.270 45.969 1.00 62.24 S ATOM 2719 SG CYS B 226 68.589 56.888 48.133 1.00 45.60 S ATOM 3019 SG CYS B 261 52.168 29.167 55.441 1.00 72.40 S ATOM 3149 SG CYS B 279 51.680 32.793 53.949 1.00 57.00 S ATOM 4539 SG CYS B 452 82.274 22.861 10.711 1.00175.36 S ATOM 4653 SG CYS B 477 82.748 21.743 14.453 1.00165.94 S ATOM 4695 SG CYS B 484 82.697 25.506 13.439 1.00167.05 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 95 " occ=0.53 ... (18 atoms not shown) pdb=" NE2BHIS B 95 " occ=0.47 Time building chain proxies: 1.89, per 1000 atoms: 0.33 Number of scatterers: 5808 At special positions: 0 Unit cell: (99.7332, 111.53, 105.095, 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 S 52 16.00 P 35 15.00 Mg 1 11.99 F 1 9.00 O 1164 8.00 N 989 7.00 C 3561 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: 2.69 Conformation dependent library (CDL) restraints added in 464.0 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 A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 207 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 261 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 279 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 452 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 477 " Number of angles added : 17 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 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: 22 helices and 9 sheets defined 30.8% alpha, 17.3% beta 17 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 85 through 89 removed outlier: 4.309A 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 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 143 through 148 removed outlier: 5.066A pdb=" N HIS B 148 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.701A pdb=" N MET B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 154' Processing helix chain 'B' and resid 158 through 175 removed outlier: 4.017A pdb=" N ILE B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 4.117A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.508A 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 252 through 258 Processing helix chain 'B' and resid 269 through 287 removed outlier: 3.509A pdb=" N VAL B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.666A pdb=" N ALA B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 484 through 505 Processing helix chain 'B' and resid 515 through 523 removed outlier: 4.022A pdb=" N TRP B 520 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 4.432A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.656A pdb=" N TYR B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 118 removed outlier: 7.032A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 118 removed outlier: 7.032A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA7, first strand: chain 'B' and resid 364 through 365 removed outlier: 3.712A pdb=" N GLU B 364 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 329 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR B 351 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B 331 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 328 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU B 383 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS B 330 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TRP B 385 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 332 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS B 382 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N CYS B 399 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE B 384 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE B 401 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER B 396 " --> pdb=" O TYR B 511 " (cutoff:3.500A) 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: 6.368A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 169 hydrogen bonds defined for protein. 450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1567 1.33 - 1.45: 1350 1.45 - 1.57: 2977 1.57 - 1.69: 67 1.69 - 1.81: 68 Bond restraints: 6029 Sorted by residual: bond pdb=" O3 EIF C 101 " pdb=" P EIF C 101 " ideal model delta sigma weight residual 1.670 1.519 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL B 341 " pdb=" CA VAL B 341 " ideal model delta sigma weight residual 1.456 1.496 -0.041 8.60e-03 1.35e+04 2.22e+01 bond pdb=" N EIF C 101 " pdb=" C6 EIF C 101 " ideal model delta sigma weight residual 1.440 1.370 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O4 EIF C 101 " pdb=" P EIF C 101 " ideal model delta sigma weight residual 1.463 1.517 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C7 EIF C 101 " pdb=" C8 EIF C 101 " ideal model delta sigma weight residual 1.430 1.376 0.054 2.00e-02 2.50e+03 7.32e+00 ... (remaining 6024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 8260 2.63 - 5.25: 90 5.25 - 7.88: 6 7.88 - 10.51: 0 10.51 - 13.14: 3 Bond angle restraints: 8359 Sorted by residual: angle pdb=" O3 EIF C 101 " pdb=" P EIF C 101 " pdb=" O4 EIF C 101 " ideal model delta sigma weight residual 128.40 115.26 13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CA VAL B 341 " pdb=" C VAL B 341 " pdb=" O VAL B 341 " ideal model delta sigma weight residual 120.88 118.21 2.67 6.80e-01 2.16e+00 1.54e+01 angle pdb=" CA VAL B 341 " pdb=" C VAL B 341 " pdb=" N PRO B 342 " ideal model delta sigma weight residual 118.12 121.27 -3.15 8.10e-01 1.52e+00 1.51e+01 angle pdb=" O1 EIF C 101 " pdb=" P EIF C 101 " pdb=" O4 EIF C 101 " ideal model delta sigma weight residual 117.72 106.61 11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" O EIF C 101 " pdb=" C2 EIF C 101 " pdb=" C3 EIF C 101 " ideal model delta sigma weight residual 105.13 115.79 -10.66 3.00e+00 1.11e-01 1.26e+01 ... (remaining 8354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3314 17.63 - 35.26: 183 35.26 - 52.90: 45 52.90 - 70.53: 29 70.53 - 88.16: 13 Dihedral angle restraints: 3584 sinusoidal: 1711 harmonic: 1873 Sorted by residual: dihedral pdb=" CA CYS B 356 " pdb=" C CYS B 356 " pdb=" N SER B 357 " pdb=" CA SER B 357 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 133 " pdb=" C PHE B 133 " pdb=" N SER B 134 " pdb=" CA SER B 134 " ideal model delta harmonic sigma weight residual -180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA VAL B 91 " pdb=" C VAL B 91 " pdb=" N GLU B 92 " pdb=" CA GLU B 92 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 862 0.081 - 0.161: 83 0.161 - 0.242: 1 0.242 - 0.323: 0 0.323 - 0.403: 1 Chirality restraints: 947 Sorted by residual: chirality pdb=" C2 EIF C 101 " pdb=" O EIF C 101 " pdb=" C1 EIF C 101 " pdb=" C3 EIF C 101 " both_signs ideal model delta sigma weight residual False -2.89 -2.49 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA VAL B 341 " pdb=" N VAL B 341 " pdb=" C VAL B 341 " pdb=" CB VAL B 341 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" C5 EIF C 101 " pdb=" N EIF C 101 " pdb=" C1 EIF C 101 " pdb=" O5 EIF C 101 " both_signs ideal model delta sigma weight residual False -2.55 -2.39 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 944 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BHIS B 95 " 0.027 2.00e-02 2.50e+03 5.50e-02 3.03e+01 pdb=" C BHIS B 95 " -0.095 2.00e-02 2.50e+03 pdb=" O BHIS B 95 " 0.035 2.00e-02 2.50e+03 pdb=" N ALA B 96 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 488 " -0.012 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C ALA B 488 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA B 488 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN B 489 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 20 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.19e+00 pdb=" C PRO B 20 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO B 20 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 21 " -0.010 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 34 2.59 - 3.17: 4599 3.17 - 3.75: 9250 3.75 - 4.32: 13226 4.32 - 4.90: 20892 Nonbonded interactions: 48001 Sorted by model distance: nonbonded pdb=" O ASN B 478 " pdb=" OD1 ASN B 478 " model vdw 2.018 3.040 nonbonded pdb=" OD1 ASP B 324 " pdb=" OH TYR B 511 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR B 472 " pdb=" OH TYR B 491 " model vdw 2.314 3.040 nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.326 2.170 nonbonded pdb=" O TYR B 370 " pdb=" OG SER B 374 " model vdw 2.337 3.040 ... (remaining 47996 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=0.47 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: 3.170 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: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.010 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.006 0.192 6050 Z= 0.302 Angle : 0.860 32.279 8376 Z= 0.472 Chirality : 0.046 0.403 947 Planarity : 0.006 0.055 940 Dihedral : 14.106 88.162 2382 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.29 (0.33), residues: 639 helix: 0.05 (0.42), residues: 146 sheet: -1.12 (0.51), residues: 87 loop : 0.05 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.011 0.002 TYR B 420 PHE 0.021 0.002 PHE B 133 TRP 0.016 0.002 TRP B 227 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.29 ( 6029) covalent geometry : angle 0.73576 / 0.46 ( 8359) hydrogen bonds : bond 0.14439 / 10.03 ( 201) hydrogen bonds : angle 6.22886 / 4.41 ( 530) metal coordination : bond 0.04461 / 2.51 ( 20) metal coordination : angle 9.89633 / 8.66 ( 17) Misc. bond : bond 0.03967 / 2.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.210 Fit side-chains REVERT: A 5 THR cc_start: 0.8165 (m) cc_final: 0.7706 (m) REVERT: A 53 GLN cc_start: 0.8409 (mt0) cc_final: 0.8139 (mt0) REVERT: A 101 THR cc_start: 0.8528 (t) cc_final: 0.7939 (m) REVERT: B 49 MET cc_start: 0.7994 (ttp) cc_final: 0.7778 (ttp) REVERT: B 61 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8078 (mtpp) REVERT: B 76 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7743 (ptm160) REVERT: B 77 GLU cc_start: 0.7115 (mp0) cc_final: 0.6794 (mp0) REVERT: B 92 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 126 ASP cc_start: 0.7854 (t70) cc_final: 0.7649 (m-30) REVERT: B 154 TYR cc_start: 0.8261 (m-80) cc_final: 0.7848 (m-80) REVERT: B 175 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8102 (ttmm) REVERT: B 304 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7241 (mmtt) REVERT: B 313 GLN cc_start: 0.7693 (tt0) cc_final: 0.7464 (tt0) REVERT: B 318 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7484 (ttpp) REVERT: B 339 LYS cc_start: 0.7505 (mtpt) cc_final: 0.7251 (mtmm) REVERT: B 347 GLU cc_start: 0.6584 (mm-30) cc_final: 0.6304 (mm-30) REVERT: B 349 LYS cc_start: 0.7269 (mttt) cc_final: 0.6783 (mttt) REVERT: B 352 ASP cc_start: 0.5486 (t0) cc_final: 0.4883 (t70) REVERT: B 492 ARG cc_start: 0.7303 (mtm180) cc_final: 0.6867 (mtm110) REVERT: B 511 TYR cc_start: 0.7593 (p90) cc_final: 0.7070 (p90) outliers start: 0 outliers final: 1 residues processed: 154 average time/residue: 0.4780 time to fit residues: 77.0643 Evaluate side-chains 127 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 330 HIS B 438 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.141651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110788 restraints weight = 12548.179| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.28 r_work: 0.3269 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 6050 Z= 0.168 Angle : 0.606 14.397 8376 Z= 0.307 Chirality : 0.042 0.148 947 Planarity : 0.005 0.044 940 Dihedral : 13.652 87.569 1240 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.63 % Allowed : 13.02 % Favored : 85.35 % 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: 0.01 (0.34), residues: 639 helix: 0.65 (0.44), residues: 146 sheet: -1.07 (0.53), residues: 81 loop : 0.11 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 205 TYR 0.020 0.002 TYR B 447 PHE 0.018 0.002 PHE B 133 TRP 0.011 0.002 TRP B 520 HIS 0.009 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 6029) covalent geometry : angle 0.56359 / 0.30 ( 8359) hydrogen bonds : bond 0.04633 / 3.11 ( 201) hydrogen bonds : angle 4.54652 / 3.22 ( 530) metal coordination : bond 0.02155 / 1.29 ( 20) metal coordination : angle 4.95671 / 2.92 ( 17) Misc. bond : bond 0.00454 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8255 (m) cc_final: 0.7823 (m) REVERT: A 101 THR cc_start: 0.8570 (t) cc_final: 0.8018 (m) REVERT: B 49 MET cc_start: 0.7940 (ttp) cc_final: 0.7671 (ttp) REVERT: B 61 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8136 (mtpp) REVERT: B 77 GLU cc_start: 0.7437 (mp0) cc_final: 0.7201 (mp0) REVERT: B 92 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 154 TYR cc_start: 0.8281 (m-80) cc_final: 0.7891 (m-80) REVERT: B 231 ILE cc_start: 0.8492 (mm) cc_final: 0.8163 (tp) REVERT: B 301 ASP cc_start: 0.7633 (m-30) cc_final: 0.7357 (m-30) REVERT: B 324 ASP cc_start: 0.7542 (m-30) cc_final: 0.7270 (m-30) REVERT: B 349 LYS cc_start: 0.8115 (mttt) cc_final: 0.7848 (mtmm) REVERT: B 352 ASP cc_start: 0.6745 (t0) cc_final: 0.6133 (t0) REVERT: B 520 TRP cc_start: 0.8032 (m100) cc_final: 0.7825 (m-90) outliers start: 9 outliers final: 3 residues processed: 135 average time/residue: 0.4596 time to fit residues: 64.8776 Evaluate side-chains 128 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN A 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111692 restraints weight = 8261.251| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.76 r_work: 0.3309 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6050 Z= 0.211 Angle : 0.615 10.102 8376 Z= 0.310 Chirality : 0.043 0.154 947 Planarity : 0.005 0.044 940 Dihedral : 13.399 73.728 1238 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.71 % Allowed : 15.19 % Favored : 82.10 % 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: 0.08 (0.34), residues: 639 helix: 0.76 (0.44), residues: 146 sheet: -0.98 (0.52), residues: 81 loop : 0.11 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 492 TYR 0.020 0.002 TYR B 420 PHE 0.030 0.002 PHE B 350 TRP 0.015 0.002 TRP B 520 HIS 0.006 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 ( 6029) covalent geometry : angle 0.58012 / 0.31 ( 8359) hydrogen bonds : bond 0.04730 / 3.22 ( 201) hydrogen bonds : angle 4.39969 / 3.11 ( 530) metal coordination : bond 0.01937 / 1.23 ( 20) metal coordination : angle 4.58325 / 2.75 ( 17) Misc. bond : bond 0.00157 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8305 (m) cc_final: 0.7894 (m) REVERT: A 58 THR cc_start: 0.8377 (t) cc_final: 0.8149 (p) REVERT: A 122 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8377 (mmm) REVERT: B 49 MET cc_start: 0.7829 (ttp) cc_final: 0.7580 (ttp) REVERT: B 61 LYS cc_start: 0.8302 (mtpt) cc_final: 0.8056 (mtpp) REVERT: B 77 GLU cc_start: 0.7274 (mp0) cc_final: 0.7054 (mp0) REVERT: B 92 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 154 TYR cc_start: 0.8151 (m-80) cc_final: 0.7760 (m-80) REVERT: B 169 MET cc_start: 0.8391 (ttp) cc_final: 0.8088 (OUTLIER) REVERT: B 301 ASP cc_start: 0.7532 (m-30) cc_final: 0.7280 (m-30) REVERT: B 318 LYS cc_start: 0.8345 (ttmm) cc_final: 0.8137 (tttp) REVERT: B 324 ASP cc_start: 0.7392 (m-30) cc_final: 0.6956 (m-30) REVERT: B 349 LYS cc_start: 0.8007 (mttt) cc_final: 0.7754 (mtmm) REVERT: B 352 ASP cc_start: 0.6568 (t0) cc_final: 0.5984 (t0) REVERT: B 492 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7284 (mtm110) REVERT: B 520 TRP cc_start: 0.8109 (m100) cc_final: 0.7881 (m-90) outliers start: 15 outliers final: 8 residues processed: 132 average time/residue: 0.4408 time to fit residues: 60.9911 Evaluate side-chains 129 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.0570 chunk 39 optimal weight: 0.0570 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 313 GLN B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110385 restraints weight = 16562.535| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.68 r_work: 0.3256 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6050 Z= 0.128 Angle : 0.563 10.323 8376 Z= 0.287 Chirality : 0.040 0.155 947 Planarity : 0.005 0.050 940 Dihedral : 13.280 73.788 1238 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.45 % Allowed : 17.18 % Favored : 81.37 % 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: 0.14 (0.34), residues: 639 helix: 0.84 (0.45), residues: 146 sheet: -0.94 (0.53), residues: 81 loop : 0.14 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 400 TYR 0.019 0.001 TYR B 447 PHE 0.042 0.002 PHE B 350 TRP 0.014 0.001 TRP B 385 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6029) covalent geometry : angle 0.53597 / 0.28 ( 8359) hydrogen bonds : bond 0.04073 / 2.73 ( 201) hydrogen bonds : angle 4.23562 / 3.00 ( 530) metal coordination : bond 0.01171 / 0.77 ( 20) metal coordination : angle 3.84018 / 2.31 ( 17) Misc. bond : bond 0.00160 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8262 (m) cc_final: 0.7865 (m) REVERT: A 58 THR cc_start: 0.8265 (t) cc_final: 0.8055 (p) REVERT: A 66 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 101 THR cc_start: 0.8416 (t) cc_final: 0.7958 (m) REVERT: B 49 MET cc_start: 0.7743 (ttp) cc_final: 0.7500 (ttp) REVERT: B 77 GLU cc_start: 0.7120 (mp0) cc_final: 0.6912 (mp0) REVERT: B 126 ASP cc_start: 0.7688 (m-30) cc_final: 0.7426 (m-30) REVERT: B 153 MET cc_start: 0.8622 (mmm) cc_final: 0.8330 (mmp) REVERT: B 154 TYR cc_start: 0.8090 (m-80) cc_final: 0.7704 (m-80) REVERT: B 169 MET cc_start: 0.8325 (ttp) cc_final: 0.8020 (ptm) REVERT: B 318 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8068 (tttp) REVERT: B 324 ASP cc_start: 0.7212 (m-30) cc_final: 0.6799 (m-30) REVERT: B 349 LYS cc_start: 0.7928 (mttt) cc_final: 0.7678 (mppt) REVERT: B 352 ASP cc_start: 0.6427 (t0) cc_final: 0.5848 (t0) REVERT: B 400 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7878 (mtp180) REVERT: B 492 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7125 (mtm110) REVERT: B 520 TRP cc_start: 0.8063 (m100) cc_final: 0.7834 (m-90) outliers start: 8 outliers final: 2 residues processed: 126 average time/residue: 0.5267 time to fit residues: 69.4082 Evaluate side-chains 122 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain B residue 354 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.0070 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 17 optimal weight: 0.0270 chunk 35 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 313 GLN B 373 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112047 restraints weight = 11939.313| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.22 r_work: 0.3300 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6050 Z= 0.121 Angle : 0.559 9.139 8376 Z= 0.285 Chirality : 0.040 0.161 947 Planarity : 0.004 0.045 940 Dihedral : 13.232 73.795 1238 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.63 % Allowed : 18.63 % Favored : 79.75 % 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: 0.18 (0.34), residues: 639 helix: 0.82 (0.44), residues: 146 sheet: -0.93 (0.53), residues: 81 loop : 0.19 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 400 TYR 0.015 0.001 TYR B 420 PHE 0.027 0.001 PHE B 444 TRP 0.013 0.001 TRP B 385 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6029) covalent geometry : angle 0.53727 / 0.28 ( 8359) hydrogen bonds : bond 0.03968 / 2.66 ( 201) hydrogen bonds : angle 4.12217 / 2.92 ( 530) metal coordination : bond 0.01084 / 0.71 ( 20) metal coordination : angle 3.42886 / 2.07 ( 17) Misc. bond : bond 0.00098 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8279 (m) cc_final: 0.7868 (m) REVERT: A 58 THR cc_start: 0.8370 (t) cc_final: 0.8149 (p) REVERT: A 66 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 101 THR cc_start: 0.8447 (t) cc_final: 0.8005 (m) REVERT: B 49 MET cc_start: 0.7926 (ttp) cc_final: 0.7655 (ttp) REVERT: B 126 ASP cc_start: 0.7872 (m-30) cc_final: 0.7637 (m-30) REVERT: B 153 MET cc_start: 0.8632 (mmm) cc_final: 0.8358 (mmp) REVERT: B 154 TYR cc_start: 0.8172 (m-80) cc_final: 0.7780 (m-80) REVERT: B 169 MET cc_start: 0.8464 (ttp) cc_final: 0.8109 (ptm) REVERT: B 318 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8213 (tttp) REVERT: B 324 ASP cc_start: 0.7424 (m-30) cc_final: 0.6944 (m-30) REVERT: B 400 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7964 (mtp180) REVERT: B 492 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7351 (mtm110) REVERT: B 520 TRP cc_start: 0.8146 (m100) cc_final: 0.7902 (m-90) outliers start: 9 outliers final: 4 residues processed: 126 average time/residue: 0.4400 time to fit residues: 57.8902 Evaluate side-chains 119 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 339 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 313 GLN B 354 GLN B 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109652 restraints weight = 13918.411| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.43 r_work: 0.3261 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6050 Z= 0.212 Angle : 0.599 10.165 8376 Z= 0.307 Chirality : 0.042 0.137 947 Planarity : 0.004 0.043 940 Dihedral : 13.250 73.773 1238 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.53 % Allowed : 18.44 % Favored : 79.02 % 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: -0.15 (0.34), residues: 639 helix: 0.39 (0.42), residues: 159 sheet: -1.03 (0.52), residues: 81 loop : 0.01 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 400 TYR 0.020 0.002 TYR B 420 PHE 0.020 0.002 PHE B 444 TRP 0.017 0.002 TRP B 520 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.21 ( 6029) covalent geometry : angle 0.57251 / 0.30 ( 8359) hydrogen bonds : bond 0.04529 / 3.06 ( 201) hydrogen bonds : angle 4.24051 / 2.98 ( 530) metal coordination : bond 0.01374 / 0.85 ( 20) metal coordination : angle 3.92036 / 2.37 ( 17) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8280 (m) cc_final: 0.7911 (m) REVERT: A 58 THR cc_start: 0.8251 (t) cc_final: 0.8026 (p) REVERT: A 101 THR cc_start: 0.8432 (t) cc_final: 0.7989 (m) REVERT: B 49 MET cc_start: 0.7705 (ttp) cc_final: 0.7469 (ttp) REVERT: B 57 MET cc_start: 0.8505 (mmt) cc_final: 0.8302 (mmm) REVERT: B 122 THR cc_start: 0.8214 (m) cc_final: 0.7890 (t) REVERT: B 126 ASP cc_start: 0.7600 (m-30) cc_final: 0.7349 (m-30) REVERT: B 153 MET cc_start: 0.8613 (mmm) cc_final: 0.8332 (mmp) REVERT: B 154 TYR cc_start: 0.8078 (m-80) cc_final: 0.7746 (m-80) REVERT: B 254 GLN cc_start: 0.8034 (tt0) cc_final: 0.7798 (tt0) REVERT: B 318 LYS cc_start: 0.8253 (ttmm) cc_final: 0.8045 (tttp) REVERT: B 324 ASP cc_start: 0.7214 (m-30) cc_final: 0.6724 (m-30) REVERT: B 447 TYR cc_start: 0.6974 (t80) cc_final: 0.6758 (t80) REVERT: B 492 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7103 (mtm110) REVERT: B 520 TRP cc_start: 0.8147 (m100) cc_final: 0.7873 (m-90) outliers start: 14 outliers final: 6 residues processed: 130 average time/residue: 0.5133 time to fit residues: 69.6665 Evaluate side-chains 124 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 20 optimal weight: 0.2980 chunk 27 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 GLN B 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.141454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110056 restraints weight = 14808.477| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.53 r_work: 0.3262 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6050 Z= 0.157 Angle : 0.576 9.423 8376 Z= 0.293 Chirality : 0.041 0.137 947 Planarity : 0.005 0.048 940 Dihedral : 13.219 73.785 1238 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.45 % Allowed : 20.25 % Favored : 78.30 % 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: -0.10 (0.34), residues: 639 helix: 0.51 (0.43), residues: 153 sheet: -0.97 (0.54), residues: 81 loop : -0.01 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 400 TYR 0.020 0.001 TYR B 447 PHE 0.017 0.002 PHE B 444 TRP 0.016 0.002 TRP B 385 HIS 0.007 0.001 HIS B 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 6029) covalent geometry : angle 0.55039 / 0.29 ( 8359) hydrogen bonds : bond 0.04247 / 2.85 ( 201) hydrogen bonds : angle 4.19728 / 2.96 ( 530) metal coordination : bond 0.01104 / 0.72 ( 20) metal coordination : angle 3.82814 / 2.27 ( 17) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8274 (m) cc_final: 0.7902 (m) REVERT: A 58 THR cc_start: 0.8225 (t) cc_final: 0.8007 (p) REVERT: B 14 VAL cc_start: 0.8458 (t) cc_final: 0.8201 (m) REVERT: B 57 MET cc_start: 0.8509 (mmt) cc_final: 0.8288 (mmm) REVERT: B 76 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7713 (ttm170) REVERT: B 122 THR cc_start: 0.8215 (m) cc_final: 0.7881 (t) REVERT: B 126 ASP cc_start: 0.7633 (m-30) cc_final: 0.7381 (m-30) REVERT: B 153 MET cc_start: 0.8599 (mmm) cc_final: 0.8338 (mmp) REVERT: B 154 TYR cc_start: 0.8082 (m-80) cc_final: 0.7695 (m-80) REVERT: B 169 MET cc_start: 0.8331 (ttp) cc_final: 0.8025 (ptm) REVERT: B 254 GLN cc_start: 0.8034 (tt0) cc_final: 0.7812 (tt0) REVERT: B 313 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: B 318 LYS cc_start: 0.8269 (ttmm) cc_final: 0.8057 (tttp) REVERT: B 324 ASP cc_start: 0.7230 (m-30) cc_final: 0.6727 (m-30) REVERT: B 329 LEU cc_start: 0.8026 (tt) cc_final: 0.7100 (tp) REVERT: B 349 LYS cc_start: 0.7908 (mttt) cc_final: 0.7660 (mppt) REVERT: B 400 ARG cc_start: 0.8106 (ttt-90) cc_final: 0.7815 (mtp180) REVERT: B 492 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7101 (mtm110) REVERT: B 520 TRP cc_start: 0.8149 (m100) cc_final: 0.7889 (m-90) outliers start: 8 outliers final: 5 residues processed: 124 average time/residue: 0.5001 time to fit residues: 65.0409 Evaluate side-chains 125 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 43 optimal weight: 0.0980 chunk 42 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.0670 overall best weight: 0.1214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110970 restraints weight = 15647.327| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.61 r_work: 0.3269 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6050 Z= 0.103 Angle : 0.535 8.766 8376 Z= 0.275 Chirality : 0.039 0.135 947 Planarity : 0.004 0.043 940 Dihedral : 13.172 73.808 1238 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.90 % Allowed : 20.98 % Favored : 78.12 % 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: 0.02 (0.34), residues: 639 helix: 0.77 (0.43), residues: 153 sheet: -1.16 (0.52), residues: 88 loop : 0.10 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 400 TYR 0.014 0.001 TYR B 420 PHE 0.017 0.001 PHE B 444 TRP 0.016 0.001 TRP B 385 HIS 0.008 0.001 HIS B 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 6029) covalent geometry : angle 0.51280 / 0.27 ( 8359) hydrogen bonds : bond 0.03883 / 2.60 ( 201) hydrogen bonds : angle 4.07580 / 2.88 ( 530) metal coordination : bond 0.00981 / 0.64 ( 20) metal coordination : angle 3.39712 / 2.03 ( 17) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8289 (m) cc_final: 0.7890 (m) REVERT: B 14 VAL cc_start: 0.8455 (t) cc_final: 0.8215 (m) REVERT: B 57 MET cc_start: 0.8522 (mmt) cc_final: 0.8306 (mmm) REVERT: B 122 THR cc_start: 0.8189 (m) cc_final: 0.7886 (t) REVERT: B 126 ASP cc_start: 0.7637 (m-30) cc_final: 0.7388 (m-30) REVERT: B 153 MET cc_start: 0.8580 (mmm) cc_final: 0.8346 (mmp) REVERT: B 154 TYR cc_start: 0.8035 (m-80) cc_final: 0.7651 (m-80) REVERT: B 169 MET cc_start: 0.8341 (ttp) cc_final: 0.8044 (ptm) REVERT: B 254 GLN cc_start: 0.8068 (tt0) cc_final: 0.7831 (tt0) REVERT: B 318 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8061 (tttp) REVERT: B 324 ASP cc_start: 0.7237 (m-30) cc_final: 0.6821 (m-30) REVERT: B 329 LEU cc_start: 0.8018 (tt) cc_final: 0.7177 (tp) REVERT: B 349 LYS cc_start: 0.7900 (mttt) cc_final: 0.7686 (mppt) REVERT: B 400 ARG cc_start: 0.8106 (ttt-90) cc_final: 0.7817 (mtp180) REVERT: B 492 ARG cc_start: 0.7522 (mtm110) cc_final: 0.7091 (mtm110) REVERT: B 520 TRP cc_start: 0.8135 (m100) cc_final: 0.7880 (m-90) outliers start: 5 outliers final: 3 residues processed: 125 average time/residue: 0.5099 time to fit residues: 66.5792 Evaluate side-chains 122 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 55 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 overall best weight: 0.2556 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.142754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110693 restraints weight = 15919.756| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.63 r_work: 0.3262 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6050 Z= 0.125 Angle : 0.548 8.413 8376 Z= 0.280 Chirality : 0.039 0.137 947 Planarity : 0.004 0.043 940 Dihedral : 13.126 73.791 1238 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.72 % Allowed : 20.98 % Favored : 78.30 % 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: 0.07 (0.34), residues: 639 helix: 0.88 (0.43), residues: 153 sheet: -1.11 (0.52), residues: 88 loop : 0.10 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 400 TYR 0.018 0.001 TYR B 447 PHE 0.014 0.001 PHE B 444 TRP 0.010 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 6029) covalent geometry : angle 0.52828 / 0.28 ( 8359) hydrogen bonds : bond 0.03928 / 2.62 ( 201) hydrogen bonds : angle 4.06665 / 2.86 ( 530) metal coordination : bond 0.00896 / 0.59 ( 20) metal coordination : angle 3.24556 / 1.93 ( 17) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8372 (m) cc_final: 0.7993 (m) REVERT: B 57 MET cc_start: 0.8533 (mmt) cc_final: 0.8303 (mmm) REVERT: B 122 THR cc_start: 0.8166 (m) cc_final: 0.7871 (t) REVERT: B 126 ASP cc_start: 0.7622 (m-30) cc_final: 0.7375 (m-30) REVERT: B 153 MET cc_start: 0.8561 (mmm) cc_final: 0.8325 (mmp) REVERT: B 154 TYR cc_start: 0.8024 (m-80) cc_final: 0.7614 (m-80) REVERT: B 169 MET cc_start: 0.8347 (ttp) cc_final: 0.8104 (OUTLIER) REVERT: B 195 MET cc_start: 0.8260 (mtt) cc_final: 0.8035 (mtt) REVERT: B 254 GLN cc_start: 0.8048 (tt0) cc_final: 0.7809 (tt0) REVERT: B 318 LYS cc_start: 0.8304 (ttmm) cc_final: 0.8090 (tttp) REVERT: B 324 ASP cc_start: 0.7239 (m-30) cc_final: 0.6760 (m-30) REVERT: B 400 ARG cc_start: 0.8128 (ttt-90) cc_final: 0.7840 (mtp180) REVERT: B 447 TYR cc_start: 0.7117 (t80) cc_final: 0.6880 (t80) REVERT: B 492 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7107 (mtm110) REVERT: B 520 TRP cc_start: 0.8166 (m100) cc_final: 0.7902 (m-90) outliers start: 4 outliers final: 5 residues processed: 124 average time/residue: 0.5264 time to fit residues: 68.2956 Evaluate side-chains 123 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 57 optimal weight: 0.2980 chunk 42 optimal weight: 0.2980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.142266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109394 restraints weight = 20972.145| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.07 r_work: 0.3222 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6050 Z= 0.155 Angle : 0.559 8.458 8376 Z= 0.286 Chirality : 0.040 0.162 947 Planarity : 0.004 0.043 940 Dihedral : 13.123 73.795 1238 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.45 % Allowed : 20.07 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.34), residues: 639 helix: 0.83 (0.43), residues: 153 sheet: -1.06 (0.52), residues: 88 loop : 0.08 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 400 TYR 0.019 0.001 TYR B 447 PHE 0.016 0.002 PHE B 133 TRP 0.015 0.002 TRP B 385 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 ( 6029) covalent geometry : angle 0.53923 / 0.28 ( 8359) hydrogen bonds : bond 0.04107 / 2.75 ( 201) hydrogen bonds : angle 4.08003 / 2.86 ( 530) metal coordination : bond 0.00936 / 0.61 ( 20) metal coordination : angle 3.32974 / 2.00 ( 17) Misc. bond : bond 0.00003 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8374 (m) cc_final: 0.8006 (m) REVERT: A 122 MET cc_start: 0.8738 (mmm) cc_final: 0.8518 (mpp) REVERT: B 57 MET cc_start: 0.8563 (mmt) cc_final: 0.8336 (mmm) REVERT: B 122 THR cc_start: 0.8205 (m) cc_final: 0.7882 (t) REVERT: B 153 MET cc_start: 0.8564 (mmm) cc_final: 0.8323 (mmp) REVERT: B 154 TYR cc_start: 0.8077 (m-80) cc_final: 0.7670 (m-80) REVERT: B 169 MET cc_start: 0.8378 (ttp) cc_final: 0.8127 (OUTLIER) REVERT: B 195 MET cc_start: 0.8290 (mtt) cc_final: 0.8055 (mtt) REVERT: B 254 GLN cc_start: 0.8108 (tt0) cc_final: 0.7873 (tt0) REVERT: B 318 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8133 (tttp) REVERT: B 324 ASP cc_start: 0.7339 (m-30) cc_final: 0.6852 (m-30) REVERT: B 349 LYS cc_start: 0.7990 (mttt) cc_final: 0.7685 (mtmm) REVERT: B 400 ARG cc_start: 0.8183 (ttt-90) cc_final: 0.7887 (mtp180) REVERT: B 421 VAL cc_start: 0.7991 (t) cc_final: 0.7776 (t) REVERT: B 447 TYR cc_start: 0.7119 (t80) cc_final: 0.6887 (t80) REVERT: B 492 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7257 (mtm110) REVERT: B 520 TRP cc_start: 0.8226 (m100) cc_final: 0.7951 (m-90) outliers start: 8 outliers final: 8 residues processed: 126 average time/residue: 0.5030 time to fit residues: 66.3914 Evaluate side-chains 128 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 28 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.141750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111877 restraints weight = 9635.398| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.95 r_work: 0.3305 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6050 Z= 0.186 Angle : 0.578 8.732 8376 Z= 0.296 Chirality : 0.042 0.194 947 Planarity : 0.004 0.043 940 Dihedral : 13.141 73.848 1238 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.08 % Allowed : 20.43 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.34), residues: 639 helix: 0.88 (0.44), residues: 147 sheet: -1.05 (0.52), residues: 88 loop : 0.02 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 400 TYR 0.020 0.001 TYR B 447 PHE 0.018 0.002 PHE B 133 TRP 0.017 0.002 TRP B 520 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 ( 6029) covalent geometry : angle 0.55604 / 0.29 ( 8359) hydrogen bonds : bond 0.04375 / 2.93 ( 201) hydrogen bonds : angle 4.15114 / 2.91 ( 530) metal coordination : bond 0.00992 / 0.64 ( 20) metal coordination : angle 3.53989 / 2.12 ( 17) Misc. bond : bond 0.00011 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.61 seconds wall clock time: 43 minutes 12.64 seconds (2592.64 seconds total)