Starting phenix.real_space_refine on Tue Aug 4 18:29:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrl_73370/08_2026/9yrl_73370.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrl_73370/08_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_73370/08_2026/9yrl_73370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrl_73370/08_2026/9yrl_73370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yrl_73370/08_2026/9yrl_73370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrl_73370/08_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-2.2rc3-6140/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: 1.78, per 1000 atoms: 0.31 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: 0.42 Conformation dependent library (CDL) restraints added in 407.2 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: 0.45 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: 1.08 Time building geometry restraints manager: 0.53 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: 8243 2.63 - 5.25: 107 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=" O5' G C 9 " pdb=" C5' G C 9 " pdb=" C4' G C 9 " ideal model delta sigma weight residual 109.40 112.88 -3.48 8.00e-01 1.56e+00 1.89e+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 ... (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: 827 0.081 - 0.161: 118 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: 3.470 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.230 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: 0.010 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- 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= 0.305 Angle : 0.899 32.279 8376 Z= 0.513 Chirality : 0.052 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 0.00545 / 0.30 ( 6029) covalent geometry : angle 0.78178 / 0.50 ( 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 : 0.201 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: 0.4515 time to fit residues: 72.6499 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 : 0.147 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.141481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110639 restraints weight = 12540.487| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.28 r_work: 0.3268 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6050 Z= 0.168 Angle : 0.601 11.670 8376 Z= 0.304 Chirality : 0.042 0.147 947 Planarity : 0.005 0.043 940 Dihedral : 13.694 88.188 1240 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.51 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: -1.09 (0.53), residues: 81 loop : 0.10 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 205 TYR 0.019 0.002 TYR B 491 PHE 0.018 0.002 PHE B 133 TRP 0.010 0.002 TRP B 520 HIS 0.008 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 6029) covalent geometry : angle 0.55759 / 0.30 ( 8359) hydrogen bonds : bond 0.04756 / 3.19 ( 201) hydrogen bonds : angle 4.57646 / 3.24 ( 530) metal coordination : bond 0.01826 / 1.14 ( 20) metal coordination : angle 4.99097 / 2.88 ( 17) Misc. bond : bond 0.00512 / 0.27 ( 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 141 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8249 (m) cc_final: 0.7814 (m) REVERT: A 101 THR cc_start: 0.8571 (t) cc_final: 0.8019 (m) REVERT: B 49 MET cc_start: 0.7958 (ttp) cc_final: 0.7687 (ttp) REVERT: B 61 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8138 (mtpp) REVERT: B 77 GLU cc_start: 0.7435 (mp0) cc_final: 0.7199 (mp0) REVERT: B 92 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 154 TYR cc_start: 0.8279 (m-80) cc_final: 0.7852 (m-80) REVERT: B 231 ILE cc_start: 0.8458 (mm) cc_final: 0.8121 (tp) REVERT: B 301 ASP cc_start: 0.7642 (m-30) cc_final: 0.7373 (m-30) REVERT: B 324 ASP cc_start: 0.7541 (m-30) cc_final: 0.7265 (m-30) REVERT: B 349 LYS cc_start: 0.8124 (mttt) cc_final: 0.7852 (mtmm) REVERT: B 352 ASP cc_start: 0.6743 (t0) cc_final: 0.6133 (t0) REVERT: B 520 TRP cc_start: 0.8023 (m100) cc_final: 0.7793 (m-90) outliers start: 9 outliers final: 3 residues processed: 135 average time/residue: 0.4269 time to fit residues: 60.3209 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 : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain B residue 74 ILE 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: 0.7980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.140971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111921 restraints weight = 8453.598| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.79 r_work: 0.3309 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 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 = 0.3164 r_free = 0.3164 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: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6050 Z= 0.185 Angle : 0.596 10.344 8376 Z= 0.302 Chirality : 0.042 0.151 947 Planarity : 0.004 0.044 940 Dihedral : 13.390 73.814 1238 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.17 % Allowed : 15.55 % Favored : 82.28 % 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: 0.81 (0.45), residues: 146 sheet: -1.01 (0.53), residues: 81 loop : 0.13 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 492 TYR 0.018 0.002 TYR B 420 PHE 0.029 0.002 PHE B 350 TRP 0.013 0.002 TRP B 520 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 ( 6029) covalent geometry : angle 0.56102 / 0.30 ( 8359) hydrogen bonds : bond 0.04596 / 3.12 ( 201) hydrogen bonds : angle 4.36187 / 3.09 ( 530) metal coordination : bond 0.01760 / 1.11 ( 20) metal coordination : angle 4.51247 / 2.67 ( 17) Misc. bond : bond 0.00050 / 0.03 ( 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 136 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8271 (m) cc_final: 0.7870 (m) REVERT: A 58 THR cc_start: 0.8371 (t) cc_final: 0.8146 (p) REVERT: A 101 THR cc_start: 0.8502 (t) cc_final: 0.7993 (m) REVERT: B 48 ASP cc_start: 0.7930 (t0) cc_final: 0.7713 (t0) REVERT: B 49 MET cc_start: 0.7846 (ttp) cc_final: 0.7595 (ttp) REVERT: B 77 GLU cc_start: 0.7286 (mp0) cc_final: 0.7074 (mp0) REVERT: B 92 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7372 (mm-30) REVERT: B 154 TYR cc_start: 0.8210 (m-80) cc_final: 0.7796 (m-80) REVERT: B 169 MET cc_start: 0.8397 (ttp) cc_final: 0.8091 (OUTLIER) REVERT: B 301 ASP cc_start: 0.7507 (m-30) cc_final: 0.7256 (m-30) REVERT: B 318 LYS cc_start: 0.8351 (ttmm) cc_final: 0.8144 (tttp) REVERT: B 324 ASP cc_start: 0.7416 (m-30) cc_final: 0.6976 (m-30) REVERT: B 352 ASP cc_start: 0.6562 (t0) cc_final: 0.5979 (t0) REVERT: B 492 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7287 (mtm110) REVERT: B 520 TRP cc_start: 0.8095 (m100) cc_final: 0.7870 (m-90) outliers start: 12 outliers final: 7 residues processed: 130 average time/residue: 0.4606 time to fit residues: 62.6900 Evaluate side-chains 127 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 129 SER Chi-restraints excluded: chain A residue 130 CYS 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: 10.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.0060 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.141422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109675 restraints weight = 16350.017| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.64 r_work: 0.3244 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 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: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6050 Z= 0.165 Angle : 0.603 10.394 8376 Z= 0.306 Chirality : 0.045 0.528 947 Planarity : 0.004 0.044 940 Dihedral : 13.333 73.851 1238 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.53 % Allowed : 16.82 % Favored : 80.65 % 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: 0.77 (0.45), residues: 146 sheet: -1.00 (0.54), residues: 81 loop : 0.11 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 400 TYR 0.022 0.002 TYR B 491 PHE 0.025 0.002 PHE B 444 TRP 0.014 0.002 TRP B 385 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 ( 6029) covalent geometry : angle 0.57435 / 0.30 ( 8359) hydrogen bonds : bond 0.04342 / 2.91 ( 201) hydrogen bonds : angle 4.31770 / 3.06 ( 530) metal coordination : bond 0.01367 / 0.88 ( 20) metal coordination : angle 4.10815 / 2.46 ( 17) Misc. bond : bond 0.00019 / 0.01 ( 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 134 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8263 (m) cc_final: 0.7862 (m) REVERT: A 58 THR cc_start: 0.8263 (t) cc_final: 0.8055 (p) REVERT: B 48 ASP cc_start: 0.7845 (t0) cc_final: 0.7542 (t0) REVERT: B 49 MET cc_start: 0.7757 (ttp) cc_final: 0.7508 (ttp) REVERT: B 77 GLU cc_start: 0.7149 (mp0) cc_final: 0.6940 (mp0) REVERT: B 154 TYR cc_start: 0.8179 (m-80) cc_final: 0.7777 (m-80) REVERT: B 169 MET cc_start: 0.8318 (ttp) cc_final: 0.8002 (ptm) REVERT: B 318 LYS cc_start: 0.8292 (ttmm) cc_final: 0.8075 (tttp) REVERT: B 324 ASP cc_start: 0.7245 (m-30) cc_final: 0.6812 (m-30) REVERT: B 352 ASP cc_start: 0.6439 (t0) cc_final: 0.5838 (t0) REVERT: B 400 ARG cc_start: 0.8115 (ttt-90) cc_final: 0.7886 (mtp180) REVERT: B 492 ARG cc_start: 0.7573 (mtm110) cc_final: 0.7234 (mtm110) REVERT: B 520 TRP cc_start: 0.8074 (m100) cc_final: 0.7849 (m-90) outliers start: 14 outliers final: 7 residues processed: 129 average time/residue: 0.5030 time to fit residues: 67.9596 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 : 0.167 ------------------------------------------------------------------------------- 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 47 LYS Chi-restraints excluded: chain B residue 113 THR 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: 0.0970 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 32 optimal weight: 0.4980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111434 restraints weight = 11740.942| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.22 r_work: 0.3287 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6050 Z= 0.141 Angle : 0.573 9.370 8376 Z= 0.293 Chirality : 0.042 0.319 947 Planarity : 0.004 0.044 940 Dihedral : 13.285 73.856 1238 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.53 % Allowed : 17.54 % Favored : 79.93 % 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: 0.13 (0.34), residues: 639 helix: 0.84 (0.44), residues: 146 sheet: -1.00 (0.53), residues: 81 loop : 0.14 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 400 TYR 0.023 0.001 TYR B 491 PHE 0.028 0.002 PHE B 444 TRP 0.014 0.002 TRP B 385 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 6029) covalent geometry : angle 0.54693 / 0.29 ( 8359) hydrogen bonds : bond 0.04124 / 2.76 ( 201) hydrogen bonds : angle 4.23973 / 3.00 ( 530) metal coordination : bond 0.01173 / 0.76 ( 20) metal coordination : angle 3.79605 / 2.24 ( 17) Misc. bond : bond 0.00034 / 0.02 ( 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 137 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8281 (m) cc_final: 0.7888 (m) REVERT: A 58 THR cc_start: 0.8382 (t) cc_final: 0.8178 (p) REVERT: A 101 THR cc_start: 0.8469 (t) cc_final: 0.8028 (m) REVERT: B 48 ASP cc_start: 0.8034 (t0) cc_final: 0.7779 (t0) REVERT: B 49 MET cc_start: 0.7970 (ttp) cc_final: 0.7728 (ttp) REVERT: B 57 MET cc_start: 0.8603 (mmt) cc_final: 0.8402 (mmm) REVERT: B 154 TYR cc_start: 0.8256 (m-80) cc_final: 0.7886 (m-80) REVERT: B 169 MET cc_start: 0.8481 (ttp) cc_final: 0.8130 (ptm) REVERT: B 324 ASP cc_start: 0.7476 (m-30) cc_final: 0.7012 (m-30) REVERT: B 352 ASP cc_start: 0.6633 (t0) cc_final: 0.5907 (t0) REVERT: B 400 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.8008 (mtp180) REVERT: B 492 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7363 (mtm110) REVERT: B 520 TRP cc_start: 0.8182 (m100) cc_final: 0.7928 (m-90) outliers start: 14 outliers final: 6 residues processed: 131 average time/residue: 0.4604 time to fit residues: 63.2359 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 : 0.196 ------------------------------------------------------------------------------- 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 339 LYS Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 17 optimal weight: 0.0870 chunk 35 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 354 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 = 0.3857 r_free = 0.3857 target = 0.142804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111088 restraints weight = 14623.047| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.52 r_work: 0.3271 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2221 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= 0.122 Angle : 0.553 9.628 8376 Z= 0.285 Chirality : 0.040 0.240 947 Planarity : 0.004 0.043 940 Dihedral : 13.227 73.857 1238 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.81 % Allowed : 18.63 % Favored : 79.57 % 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: 0.12 (0.34), residues: 639 helix: 0.99 (0.44), residues: 141 sheet: -1.23 (0.50), residues: 88 loop : 0.16 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 400 TYR 0.025 0.002 TYR B 491 PHE 0.032 0.002 PHE B 444 TRP 0.012 0.001 TRP B 385 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 6029) covalent geometry : angle 0.53032 / 0.28 ( 8359) hydrogen bonds : bond 0.04004 / 2.67 ( 201) hydrogen bonds : angle 4.08414 / 2.90 ( 530) metal coordination : bond 0.01079 / 0.71 ( 20) metal coordination : angle 3.54626 / 2.13 ( 17) Misc. bond : bond 0.00046 / 0.02 ( 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 128 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8268 (m) cc_final: 0.7894 (m) REVERT: A 66 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7479 (mm-30) REVERT: A 101 THR cc_start: 0.8409 (t) cc_final: 0.7969 (m) REVERT: B 48 ASP cc_start: 0.7861 (t0) cc_final: 0.7587 (t0) REVERT: B 49 MET cc_start: 0.7726 (ttp) cc_final: 0.7505 (ttp) REVERT: B 57 MET cc_start: 0.8532 (mmt) cc_final: 0.8310 (mmm) REVERT: B 126 ASP cc_start: 0.7743 (m-30) cc_final: 0.7401 (m-30) REVERT: B 154 TYR cc_start: 0.8109 (m-80) cc_final: 0.7759 (m-80) REVERT: B 324 ASP cc_start: 0.7282 (m-30) cc_final: 0.6892 (m-30) REVERT: B 400 ARG cc_start: 0.8119 (ttt-90) cc_final: 0.7891 (mtp180) REVERT: B 492 ARG cc_start: 0.7482 (mtm110) cc_final: 0.7085 (mtm110) REVERT: B 520 TRP cc_start: 0.8108 (m100) cc_final: 0.7857 (m-90) outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 0.4609 time to fit residues: 59.7045 Evaluate side-chains 121 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 339 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 35 optimal weight: 0.0870 chunk 43 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110378 restraints weight = 14549.587| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.48 r_work: 0.3252 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- 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 = 0.45 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: 0.7921 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6050 Z= 0.177 Angle : 0.575 9.516 8376 Z= 0.294 Chirality : 0.041 0.155 947 Planarity : 0.004 0.042 940 Dihedral : 13.221 73.793 1238 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.63 % Allowed : 19.53 % Favored : 78.84 % 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: 147 sheet: -1.17 (0.50), residues: 88 loop : 0.13 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 400 TYR 0.018 0.002 TYR B 420 PHE 0.021 0.002 PHE B 350 TRP 0.015 0.002 TRP B 520 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 6029) covalent geometry : angle 0.55018 / 0.29 ( 8359) hydrogen bonds : bond 0.04306 / 2.88 ( 201) hydrogen bonds : angle 4.15031 / 2.93 ( 530) metal coordination : bond 0.01133 / 0.73 ( 20) metal coordination : angle 3.73044 / 2.21 ( 17) Misc. bond : bond 0.00048 / 0.03 ( 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 129 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8292 (m) cc_final: 0.7915 (m) REVERT: B 14 VAL cc_start: 0.8472 (t) cc_final: 0.8214 (m) REVERT: B 48 ASP cc_start: 0.7854 (t0) cc_final: 0.7653 (t0) REVERT: B 49 MET cc_start: 0.7685 (ttp) cc_final: 0.7473 (ttp) REVERT: B 57 MET cc_start: 0.8547 (mmt) cc_final: 0.8328 (mmm) REVERT: B 126 ASP cc_start: 0.7761 (m-30) cc_final: 0.7423 (m-30) REVERT: B 154 TYR cc_start: 0.8137 (m-80) cc_final: 0.7736 (m-80) REVERT: B 169 MET cc_start: 0.8323 (ttp) cc_final: 0.8048 (ptm) REVERT: B 254 GLN cc_start: 0.8077 (tt0) cc_final: 0.7853 (tt0) REVERT: B 313 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: B 324 ASP cc_start: 0.7309 (m-30) cc_final: 0.6903 (m-30) REVERT: B 381 VAL cc_start: 0.6812 (p) cc_final: 0.6541 (p) REVERT: B 492 ARG cc_start: 0.7496 (mtm110) cc_final: 0.7114 (mtm110) REVERT: B 520 TRP cc_start: 0.8144 (m100) cc_final: 0.7871 (m-90) outliers start: 9 outliers final: 5 residues processed: 123 average time/residue: 0.4834 time to fit residues: 62.2257 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 : 0.127 ------------------------------------------------------------------------------- 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 405 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 0.0670 chunk 55 optimal weight: 0.1980 chunk 63 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 42 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 overall best weight: 0.1052 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.144024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112145 restraints weight = 15952.690| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.62 r_work: 0.3281 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6050 Z= 0.101 Angle : 0.525 8.088 8376 Z= 0.270 Chirality : 0.039 0.141 947 Planarity : 0.004 0.049 940 Dihedral : 13.146 73.923 1238 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.08 % Allowed : 19.89 % 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: 0.24 (0.34), residues: 639 helix: 1.11 (0.44), residues: 144 sheet: -1.15 (0.48), residues: 95 loop : 0.26 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 400 TYR 0.017 0.001 TYR B 447 PHE 0.022 0.001 PHE B 444 TRP 0.012 0.001 TRP B 227 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 6029) covalent geometry : angle 0.50903 / 0.27 ( 8359) hydrogen bonds : bond 0.03728 / 2.45 ( 201) hydrogen bonds : angle 3.98969 / 2.84 ( 530) metal coordination : bond 0.00885 / 0.57 ( 20) metal coordination : angle 2.90780 / 1.76 ( 17) Misc. bond : bond 0.00068 / 0.04 ( 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 126 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8334 (m) cc_final: 0.7967 (m) REVERT: A 66 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7471 (mm-30) REVERT: A 122 MET cc_start: 0.8654 (mmm) cc_final: 0.8420 (mpp) REVERT: B 14 VAL cc_start: 0.8452 (t) cc_final: 0.8200 (m) REVERT: B 57 MET cc_start: 0.8563 (mmt) cc_final: 0.8332 (mmm) REVERT: B 126 ASP cc_start: 0.7788 (m-30) cc_final: 0.7449 (m-30) REVERT: B 154 TYR cc_start: 0.8039 (m-80) cc_final: 0.7771 (m-80) REVERT: B 169 MET cc_start: 0.8326 (ttp) cc_final: 0.8034 (ptm) REVERT: B 324 ASP cc_start: 0.7276 (m-30) cc_final: 0.6886 (m-30) REVERT: B 339 LYS cc_start: 0.7874 (ttmm) cc_final: 0.7579 (mtpm) REVERT: B 400 ARG cc_start: 0.8066 (ttt-90) cc_final: 0.7844 (mtp180) REVERT: B 492 ARG cc_start: 0.7477 (mtm110) cc_final: 0.7152 (mtm110) REVERT: B 520 TRP cc_start: 0.8108 (m100) cc_final: 0.7854 (m-90) outliers start: 6 outliers final: 3 residues processed: 123 average time/residue: 0.4409 time to fit residues: 56.8249 Evaluate side-chains 118 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 325 LYS 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: 0.9990 chunk 5 optimal weight: 0.0010 chunk 29 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 37 optimal weight: 0.3980 chunk 1 optimal weight: 0.0980 chunk 55 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111248 restraints weight = 16028.780| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.62 r_work: 0.3270 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6050 Z= 0.125 Angle : 0.542 8.098 8376 Z= 0.279 Chirality : 0.039 0.137 947 Planarity : 0.004 0.042 940 Dihedral : 13.137 73.826 1238 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.08 % Allowed : 20.07 % Favored : 78.84 % 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: 0.20 (0.34), residues: 639 helix: 1.03 (0.44), residues: 147 sheet: -1.07 (0.48), residues: 95 loop : 0.22 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 400 TYR 0.014 0.001 TYR B 420 PHE 0.018 0.002 PHE B 444 TRP 0.011 0.001 TRP B 385 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 6029) covalent geometry : angle 0.52590 / 0.28 ( 8359) hydrogen bonds : bond 0.03828 / 2.53 ( 201) hydrogen bonds : angle 3.98853 / 2.82 ( 530) metal coordination : bond 0.00829 / 0.55 ( 20) metal coordination : angle 3.00199 / 1.80 ( 17) Misc. bond : bond 0.00041 / 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 124 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8359 (m) cc_final: 0.7989 (m) REVERT: A 122 MET cc_start: 0.8655 (mmm) cc_final: 0.8419 (mpp) REVERT: B 57 MET cc_start: 0.8572 (mmt) cc_final: 0.8354 (mmm) REVERT: B 122 THR cc_start: 0.8107 (m) cc_final: 0.7823 (t) REVERT: B 126 ASP cc_start: 0.7770 (m-30) cc_final: 0.7438 (m-30) REVERT: B 154 TYR cc_start: 0.8058 (m-80) cc_final: 0.7799 (m-80) REVERT: B 169 MET cc_start: 0.8342 (ttp) cc_final: 0.8054 (ptm) REVERT: B 324 ASP cc_start: 0.7251 (m-30) cc_final: 0.6764 (m-30) REVERT: B 400 ARG cc_start: 0.8114 (ttt-90) cc_final: 0.7908 (mtp180) REVERT: B 492 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7165 (mtm110) REVERT: B 520 TRP cc_start: 0.8136 (m100) cc_final: 0.7873 (m-90) outliers start: 6 outliers final: 4 residues processed: 121 average time/residue: 0.4728 time to fit residues: 59.8061 Evaluate side-chains 122 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 325 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 57 optimal weight: 0.0870 chunk 42 optimal weight: 0.5980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108928 restraints weight = 20911.811| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.08 r_work: 0.3218 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- 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 = 0.46 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 = 0.45 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: 0.7969 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6050 Z= 0.163 Angle : 0.566 8.432 8376 Z= 0.290 Chirality : 0.040 0.137 947 Planarity : 0.004 0.043 940 Dihedral : 13.148 73.878 1238 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.72 % Allowed : 19.71 % Favored : 79.57 % 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: 0.20 (0.34), residues: 639 helix: 1.03 (0.43), residues: 147 sheet: -1.03 (0.49), residues: 95 loop : 0.20 (0.33), residues: 397 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 133 TRP 0.015 0.002 TRP B 520 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 6029) covalent geometry : angle 0.54631 / 0.29 ( 8359) hydrogen bonds : bond 0.04143 / 2.76 ( 201) hydrogen bonds : angle 4.05967 / 2.86 ( 530) metal coordination : bond 0.00965 / 0.62 ( 20) metal coordination : angle 3.32108 / 1.99 ( 17) Misc. bond : bond 0.00031 / 0.02 ( 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 126 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 5 THR cc_start: 0.8361 (m) cc_final: 0.8005 (m) REVERT: A 122 MET cc_start: 0.8696 (mmm) cc_final: 0.8463 (mpp) REVERT: B 57 MET cc_start: 0.8587 (mmt) cc_final: 0.8374 (mmm) REVERT: B 122 THR cc_start: 0.8176 (m) cc_final: 0.7893 (t) REVERT: B 126 ASP cc_start: 0.7813 (m-30) cc_final: 0.7486 (m-30) REVERT: B 154 TYR cc_start: 0.8133 (m-80) cc_final: 0.7838 (m-80) REVERT: B 169 MET cc_start: 0.8379 (ttp) cc_final: 0.8138 (OUTLIER) REVERT: B 324 ASP cc_start: 0.7307 (m-30) cc_final: 0.6855 (m-30) REVERT: B 400 ARG cc_start: 0.8175 (ttt-90) cc_final: 0.7894 (mtp180) REVERT: B 421 VAL cc_start: 0.8012 (t) cc_final: 0.7804 (t) REVERT: B 447 TYR cc_start: 0.7141 (t80) cc_final: 0.6867 (t80) REVERT: B 492 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7316 (mtm110) REVERT: B 520 TRP cc_start: 0.8200 (m100) cc_final: 0.7923 (m-90) outliers start: 4 outliers final: 5 residues processed: 123 average time/residue: 0.4390 time to fit residues: 56.4526 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 : 0.129 ------------------------------------------------------------------------------- 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 325 LYS 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: 0.3980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 0.0040 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.0670 chunk 34 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 overall best weight: 0.2930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112787 restraints weight = 9587.810| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.96 r_work: 0.3317 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 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 = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6050 Z= 0.132 Angle : 0.552 8.169 8376 Z= 0.281 Chirality : 0.039 0.138 947 Planarity : 0.004 0.041 940 Dihedral : 13.137 73.863 1238 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.72 % Allowed : 19.89 % Favored : 79.39 % 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: 0.20 (0.34), residues: 639 helix: 1.05 (0.44), residues: 147 sheet: -1.06 (0.49), residues: 95 loop : 0.20 (0.33), residues: 397 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 0.018 0.001 PHE B 444 TRP 0.014 0.002 TRP B 385 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 6029) covalent geometry : angle 0.53446 / 0.28 ( 8359) hydrogen bonds : bond 0.03963 / 2.64 ( 201) hydrogen bonds : angle 4.01348 / 2.84 ( 530) metal coordination : bond 0.00854 / 0.56 ( 20) metal coordination : angle 3.10983 / 1.87 ( 17) Misc. bond : bond 0.00029 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2333.58 seconds wall clock time: 40 minutes 19.81 seconds (2419.81 seconds total)