Starting phenix.real_space_refine on Wed Mar 4 04:33:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jl1_22369/03_2026/7jl1_22369.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jl1_22369/03_2026/7jl1_22369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jl1_22369/03_2026/7jl1_22369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jl1_22369/03_2026/7jl1_22369.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jl1_22369/03_2026/7jl1_22369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jl1_22369/03_2026/7jl1_22369.map" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4056 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 1 6.06 5 Al 1 5.89 5 P 30 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 4451 2.51 5 N 1220 2.21 5 O 1383 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7132 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5184 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 25, 'TRANS': 630} Chain breaks: 6 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "X" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "Y" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 295 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna3p': 13} Chain: "B" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1319 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4362 SG CYS A 810 69.713 98.163 31.557 1.00 61.48 S ATOM 4388 SG CYS A 813 72.965 99.873 31.865 1.00 62.37 S ATOM 4728 SG CYS A 864 71.899 99.040 28.358 1.00 71.24 S ATOM 4767 SG CYS A 869 72.980 96.306 30.728 1.00 76.60 S Time building chain proxies: 2.00, per 1000 atoms: 0.28 Number of scatterers: 7132 At special positions: 0 Unit cell: (96.9088, 121.918, 67.732, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 S 41 16.00 P 30 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1383 8.00 N 1220 7.00 C 4451 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=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 233.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 813 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 869 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 864 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 810 " Number of angles added : 6 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 42.1% alpha, 14.8% beta 9 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.701A pdb=" N LYS A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 316 removed outlier: 4.653A pdb=" N ARG A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.719A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 4.118A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.583A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.583A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.616A pdb=" N GLN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 490 removed outlier: 3.515A pdb=" N TYR A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.858A pdb=" N GLU A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 558 removed outlier: 4.239A pdb=" N ARG A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.703A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 592 Processing helix chain 'A' and resid 593 through 602 removed outlier: 3.618A pdb=" N ARG A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 removed outlier: 3.669A pdb=" N VAL A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 removed outlier: 3.517A pdb=" N LYS A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 701 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 744 through 768 removed outlier: 3.682A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 768 " --> pdb=" O SER A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 774 through 794 Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 835 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.328A pdb=" N VAL A 293 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 346 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE A 295 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET A 369 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 261 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 removed outlier: 6.687A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.529A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 894 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 903 " --> pdb=" O VAL A 894 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 874 through 879 Processing sheet with id=AA6, first strand: chain 'B' and resid 272 through 274 removed outlier: 3.990A pdb=" N ILE B 426 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU B 316 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 390 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR B 400 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER B 391 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU B 398 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 301 through 303 removed outlier: 4.273A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 357 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS B 361 " --> pdb=" O LYS B 364 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1329 1.32 - 1.45: 1908 1.45 - 1.57: 3981 1.57 - 1.69: 57 1.69 - 1.81: 60 Bond restraints: 7335 Sorted by residual: bond pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F3 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.685 1.781 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" F4 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.686 1.779 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.684 1.768 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N CYS A 490 " pdb=" CA CYS A 490 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.33e-02 5.65e+03 7.06e+00 ... (remaining 7330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.88: 10052 13.88 - 27.76: 4 27.76 - 41.64: 0 41.64 - 55.53: 0 55.53 - 69.41: 2 Bond angle restraints: 10058 Sorted by residual: angle pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " pdb=" F2 ALF A2002 " ideal model delta sigma weight residual 108.68 178.09 -69.41 3.00e+00 1.11e-01 5.35e+02 angle pdb=" F3 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 109.63 177.66 -68.03 3.00e+00 1.11e-01 5.14e+02 angle pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " pdb=" F3 ALF A2002 " ideal model delta sigma weight residual 109.59 88.94 20.65 3.00e+00 1.11e-01 4.74e+01 angle pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 109.02 88.94 20.08 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 110.21 91.34 18.87 3.00e+00 1.11e-01 3.96e+01 ... (remaining 10053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 4289 35.43 - 70.85: 129 70.85 - 106.28: 11 106.28 - 141.70: 2 141.70 - 177.12: 3 Dihedral angle restraints: 4434 sinusoidal: 2015 harmonic: 2419 Sorted by residual: dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual 300.00 164.34 135.66 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O2A ADP A2001 " pdb=" O3A ADP A2001 " pdb=" PA ADP A2001 " pdb=" PB ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 56.28 -116.28 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" CA THR A 347 " pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 4431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 877 0.061 - 0.121: 251 0.121 - 0.182: 32 0.182 - 0.243: 2 0.243 - 0.303: 2 Chirality restraints: 1164 Sorted by residual: chirality pdb=" C3' G Y 4 " pdb=" C4' G Y 4 " pdb=" O3' G Y 4 " pdb=" C2' G Y 4 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' A X 2 " pdb=" C4' A X 2 " pdb=" O3' A X 2 " pdb=" C2' A X 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA LEU A 493 " pdb=" N LEU A 493 " pdb=" C LEU A 493 " pdb=" CB LEU A 493 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 1161 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A X 2 " 0.042 2.00e-02 2.50e+03 1.85e-02 9.43e+00 pdb=" N9 A X 2 " -0.041 2.00e-02 2.50e+03 pdb=" C8 A X 2 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A X 2 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A X 2 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A X 2 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A X 2 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A X 2 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A X 2 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A X 2 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A X 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 313 " 0.015 2.00e-02 2.50e+03 1.72e-02 4.46e+00 pdb=" CG HIS B 313 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS B 313 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 313 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 313 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 313 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 411 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO B 412 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " -0.028 5.00e-02 4.00e+02 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 14 2.36 - 3.00: 3988 3.00 - 3.63: 9937 3.63 - 4.27: 14913 4.27 - 4.90: 25060 Nonbonded interactions: 53912 Sorted by model distance: nonbonded pdb=" F1 ALF A2002 " pdb="MG MG A2003 " model vdw 1.727 2.120 nonbonded pdb=" O1B ADP A2001 " pdb="MG MG A2003 " model vdw 1.793 2.170 nonbonded pdb=" F4 ALF A2002 " pdb="MG MG A2003 " model vdw 1.813 2.120 nonbonded pdb=" O1B ADP A2001 " pdb=" F4 ALF A2002 " model vdw 2.014 2.990 nonbonded pdb=" O2B ADP A2001 " pdb=" F2 ALF A2002 " model vdw 2.064 2.990 ... (remaining 53907 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.011 0.114 7339 Z= 0.476 Angle : 1.385 69.407 10064 Z= 0.600 Chirality : 0.054 0.303 1164 Planarity : 0.005 0.050 1158 Dihedral : 17.187 177.125 2858 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.14 % Allowed : 6.44 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.42 (0.29), residues: 805 helix: 1.22 (0.30), residues: 302 sheet: 0.06 (0.45), residues: 144 loop : -0.35 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 296 TYR 0.031 0.003 TYR A 303 PHE 0.019 0.003 PHE A 295 TRP 0.013 0.002 TRP B 315 HIS 0.020 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.01072 ( 7335) covalent geometry : angle 1.38226 (10058) hydrogen bonds : bond 0.15475 ( 319) hydrogen bonds : angle 6.65900 ( 886) metal coordination : bond 0.00757 ( 4) metal coordination : angle 3.76063 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8412 (tppt) cc_final: 0.8197 (ttpt) REVERT: A 387 MET cc_start: 0.8925 (mmp) cc_final: 0.8701 (mmt) REVERT: A 435 ASP cc_start: 0.8639 (t0) cc_final: 0.7757 (t0) REVERT: A 492 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7656 (p0) REVERT: A 610 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7415 (mtpp) REVERT: A 690 ASP cc_start: 0.8452 (p0) cc_final: 0.8165 (p0) REVERT: A 692 ASN cc_start: 0.8152 (m-40) cc_final: 0.7544 (t0) REVERT: A 756 TYR cc_start: 0.7623 (t80) cc_final: 0.7403 (t80) REVERT: A 761 MET cc_start: 0.7522 (ttp) cc_final: 0.7241 (ttp) REVERT: A 859 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7319 (tpp80) REVERT: B 321 ASN cc_start: 0.8208 (t0) cc_final: 0.7864 (t0) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.0995 time to fit residues: 22.4872 Evaluate side-chains 131 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN A 573 ASN A 782 HIS A 876 HIS ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.160276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.127173 restraints weight = 8175.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.125863 restraints weight = 8475.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.128003 restraints weight = 8363.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.128669 restraints weight = 5141.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.128922 restraints weight = 5127.009| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7339 Z= 0.160 Angle : 0.637 7.498 10064 Z= 0.324 Chirality : 0.044 0.221 1164 Planarity : 0.004 0.038 1158 Dihedral : 16.355 163.230 1316 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.43 % Allowed : 13.16 % Favored : 84.41 % 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: 0.75 (0.30), residues: 805 helix: 1.51 (0.29), residues: 304 sheet: 0.10 (0.46), residues: 154 loop : -0.13 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 732 TYR 0.023 0.002 TYR A 541 PHE 0.016 0.001 PHE A 913 TRP 0.012 0.001 TRP A 512 HIS 0.007 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7335) covalent geometry : angle 0.62697 (10058) hydrogen bonds : bond 0.05553 ( 319) hydrogen bonds : angle 4.87035 ( 886) metal coordination : bond 0.00427 ( 4) metal coordination : angle 4.68066 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.244 Fit side-chains REVERT: A 241 PHE cc_start: 0.7971 (m-80) cc_final: 0.7750 (m-80) REVERT: A 283 LYS cc_start: 0.8529 (tppt) cc_final: 0.8035 (tttp) REVERT: A 387 MET cc_start: 0.9051 (mmp) cc_final: 0.8785 (mmt) REVERT: A 454 TYR cc_start: 0.7343 (t80) cc_final: 0.7119 (t80) REVERT: A 481 ASP cc_start: 0.8076 (m-30) cc_final: 0.7792 (m-30) REVERT: A 692 ASN cc_start: 0.8283 (m-40) cc_final: 0.7749 (t0) REVERT: A 756 TYR cc_start: 0.7517 (t80) cc_final: 0.7279 (t80) REVERT: A 761 MET cc_start: 0.7401 (ttp) cc_final: 0.7152 (ttp) REVERT: A 822 ASP cc_start: 0.8433 (m-30) cc_final: 0.7776 (t0) REVERT: B 321 ASN cc_start: 0.8054 (t0) cc_final: 0.7794 (t0) REVERT: B 362 MET cc_start: 0.7629 (mmm) cc_final: 0.7023 (mtp) outliers start: 17 outliers final: 11 residues processed: 150 average time/residue: 0.0860 time to fit residues: 17.1844 Evaluate side-chains 140 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 916 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 0.0270 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 25 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 678 GLN A 876 HIS B 313 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.165016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.132009 restraints weight = 7974.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.133209 restraints weight = 6901.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.134323 restraints weight = 6179.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.134882 restraints weight = 4568.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.135116 restraints weight = 4200.176| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7339 Z= 0.104 Angle : 0.551 6.039 10064 Z= 0.279 Chirality : 0.042 0.212 1164 Planarity : 0.003 0.040 1158 Dihedral : 16.215 164.959 1314 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.15 % Allowed : 16.88 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.30), residues: 805 helix: 1.84 (0.29), residues: 304 sheet: 0.34 (0.46), residues: 148 loop : -0.15 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 244 TYR 0.011 0.001 TYR A 303 PHE 0.014 0.001 PHE A 913 TRP 0.015 0.001 TRP B 257 HIS 0.011 0.001 HIS A 876 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 7335) covalent geometry : angle 0.54506 (10058) hydrogen bonds : bond 0.04385 ( 319) hydrogen bonds : angle 4.30266 ( 886) metal coordination : bond 0.00183 ( 4) metal coordination : angle 3.45150 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.239 Fit side-chains REVERT: A 283 LYS cc_start: 0.8486 (tppt) cc_final: 0.7975 (tttp) REVERT: A 387 MET cc_start: 0.8897 (mmp) cc_final: 0.8590 (mmt) REVERT: A 435 ASP cc_start: 0.8542 (t0) cc_final: 0.8047 (t0) REVERT: A 454 TYR cc_start: 0.7176 (t80) cc_final: 0.6968 (t80) REVERT: A 610 LYS cc_start: 0.7543 (mtpp) cc_final: 0.7252 (mttt) REVERT: A 690 ASP cc_start: 0.8236 (p0) cc_final: 0.8020 (p0) REVERT: A 692 ASN cc_start: 0.8245 (m-40) cc_final: 0.7654 (t0) REVERT: A 756 TYR cc_start: 0.7498 (t80) cc_final: 0.7207 (t80) REVERT: A 822 ASP cc_start: 0.8426 (m-30) cc_final: 0.7725 (t0) REVERT: B 335 SER cc_start: 0.8788 (t) cc_final: 0.8123 (p) REVERT: B 362 MET cc_start: 0.7500 (mmm) cc_final: 0.7008 (mtp) outliers start: 15 outliers final: 12 residues processed: 145 average time/residue: 0.0835 time to fit residues: 16.2766 Evaluate side-chains 139 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 876 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.158852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.123975 restraints weight = 8282.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.125089 restraints weight = 7702.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.126025 restraints weight = 7022.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.126283 restraints weight = 5083.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.126484 restraints weight = 4697.176| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7339 Z= 0.191 Angle : 0.611 8.032 10064 Z= 0.310 Chirality : 0.044 0.239 1164 Planarity : 0.004 0.041 1158 Dihedral : 16.178 165.748 1314 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.58 % Allowed : 18.45 % Favored : 76.97 % 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: 0.80 (0.30), residues: 805 helix: 1.69 (0.29), residues: 303 sheet: 0.10 (0.44), residues: 158 loop : -0.22 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.019 0.002 TYR A 303 PHE 0.013 0.002 PHE A 739 TRP 0.010 0.001 TRP B 257 HIS 0.006 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 7335) covalent geometry : angle 0.60037 (10058) hydrogen bonds : bond 0.05238 ( 319) hydrogen bonds : angle 4.44231 ( 886) metal coordination : bond 0.00302 ( 4) metal coordination : angle 4.66517 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8579 (tppt) cc_final: 0.8148 (ttpp) REVERT: A 387 MET cc_start: 0.9012 (mmp) cc_final: 0.8737 (mmt) REVERT: A 554 ILE cc_start: 0.8962 (mm) cc_final: 0.8551 (mt) REVERT: A 657 LYS cc_start: 0.8765 (tptm) cc_final: 0.8212 (tppt) REVERT: A 692 ASN cc_start: 0.8497 (m-40) cc_final: 0.7661 (t0) REVERT: A 756 TYR cc_start: 0.7472 (t80) cc_final: 0.7158 (t80) REVERT: A 822 ASP cc_start: 0.8332 (m-30) cc_final: 0.7679 (t0) REVERT: B 362 MET cc_start: 0.7634 (mmm) cc_final: 0.7409 (ttm) outliers start: 32 outliers final: 25 residues processed: 146 average time/residue: 0.0778 time to fit residues: 15.5114 Evaluate side-chains 148 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 678 GLN A 782 HIS A 876 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.159771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.125111 restraints weight = 8237.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.126304 restraints weight = 7623.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.127392 restraints weight = 6525.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.127598 restraints weight = 4880.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.128100 restraints weight = 4620.885| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7339 Z= 0.150 Angle : 0.576 7.679 10064 Z= 0.292 Chirality : 0.043 0.224 1164 Planarity : 0.003 0.041 1158 Dihedral : 16.120 165.460 1314 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.01 % Allowed : 20.31 % Favored : 75.68 % 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: 0.76 (0.29), residues: 805 helix: 1.74 (0.29), residues: 303 sheet: -0.02 (0.44), residues: 159 loop : -0.29 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.015 0.002 TYR A 303 PHE 0.011 0.001 PHE A 911 TRP 0.012 0.001 TRP B 257 HIS 0.007 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7335) covalent geometry : angle 0.56637 (10058) hydrogen bonds : bond 0.04824 ( 319) hydrogen bonds : angle 4.30751 ( 886) metal coordination : bond 0.00231 ( 4) metal coordination : angle 4.40638 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8617 (tppt) cc_final: 0.7973 (tttp) REVERT: A 387 MET cc_start: 0.9000 (mmp) cc_final: 0.8702 (mmt) REVERT: A 657 LYS cc_start: 0.8676 (tptm) cc_final: 0.8151 (tppt) REVERT: A 692 ASN cc_start: 0.8591 (m-40) cc_final: 0.7721 (t0) REVERT: A 756 TYR cc_start: 0.7527 (t80) cc_final: 0.7172 (t80) REVERT: A 822 ASP cc_start: 0.8335 (m-30) cc_final: 0.7515 (t0) outliers start: 28 outliers final: 25 residues processed: 145 average time/residue: 0.0885 time to fit residues: 17.5277 Evaluate side-chains 149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 71 optimal weight: 9.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.163853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.129151 restraints weight = 8242.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.130002 restraints weight = 7469.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.131391 restraints weight = 6699.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.132070 restraints weight = 4772.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.132338 restraints weight = 4462.811| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7339 Z= 0.102 Angle : 0.535 5.870 10064 Z= 0.270 Chirality : 0.041 0.210 1164 Planarity : 0.003 0.041 1158 Dihedral : 16.070 164.761 1314 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.15 % Allowed : 22.75 % Favored : 74.11 % 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: 0.90 (0.30), residues: 805 helix: 1.95 (0.29), residues: 304 sheet: 0.20 (0.45), residues: 148 loop : -0.38 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 559 TYR 0.030 0.002 TYR A 541 PHE 0.013 0.001 PHE B 414 TRP 0.015 0.001 TRP B 257 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7335) covalent geometry : angle 0.52803 (10058) hydrogen bonds : bond 0.04032 ( 319) hydrogen bonds : angle 4.03749 ( 886) metal coordination : bond 0.00200 ( 4) metal coordination : angle 3.50534 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8573 (tppt) cc_final: 0.7977 (tttp) REVERT: A 387 MET cc_start: 0.8928 (mmp) cc_final: 0.8620 (mmt) REVERT: A 692 ASN cc_start: 0.8546 (m-40) cc_final: 0.7635 (t0) REVERT: A 756 TYR cc_start: 0.7512 (t80) cc_final: 0.7129 (t80) REVERT: A 822 ASP cc_start: 0.8334 (m-30) cc_final: 0.7491 (t0) outliers start: 22 outliers final: 19 residues processed: 149 average time/residue: 0.0868 time to fit residues: 17.5111 Evaluate side-chains 151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN A 678 GLN A 876 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.160578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.126513 restraints weight = 8099.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.127765 restraints weight = 7794.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.128764 restraints weight = 6640.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.129466 restraints weight = 5041.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.129646 restraints weight = 4599.310| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7339 Z= 0.141 Angle : 0.567 7.643 10064 Z= 0.286 Chirality : 0.042 0.220 1164 Planarity : 0.003 0.041 1158 Dihedral : 15.993 165.296 1314 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.43 % Allowed : 22.75 % Favored : 73.82 % 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: 0.91 (0.29), residues: 805 helix: 1.91 (0.29), residues: 303 sheet: 0.21 (0.44), residues: 158 loop : -0.34 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 637 TYR 0.027 0.002 TYR A 541 PHE 0.009 0.001 PHE A 911 TRP 0.014 0.001 TRP B 257 HIS 0.004 0.001 HIS A 876 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7335) covalent geometry : angle 0.55759 (10058) hydrogen bonds : bond 0.04461 ( 319) hydrogen bonds : angle 4.14394 ( 886) metal coordination : bond 0.00234 ( 4) metal coordination : angle 4.14441 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.268 Fit side-chains REVERT: A 283 LYS cc_start: 0.8599 (tppt) cc_final: 0.7926 (tttp) REVERT: A 387 MET cc_start: 0.8981 (mmp) cc_final: 0.8677 (mmt) REVERT: A 612 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 756 TYR cc_start: 0.7528 (t80) cc_final: 0.7139 (t80) REVERT: A 822 ASP cc_start: 0.8296 (m-30) cc_final: 0.7483 (t0) outliers start: 24 outliers final: 19 residues processed: 135 average time/residue: 0.0823 time to fit residues: 15.2743 Evaluate side-chains 142 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 63 optimal weight: 0.0270 chunk 45 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 overall best weight: 2.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.159513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.125384 restraints weight = 8212.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.126337 restraints weight = 7725.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.127491 restraints weight = 6760.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.128140 restraints weight = 5068.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.128316 restraints weight = 4698.391| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7339 Z= 0.160 Angle : 0.584 7.966 10064 Z= 0.294 Chirality : 0.043 0.227 1164 Planarity : 0.003 0.041 1158 Dihedral : 15.964 165.276 1314 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.43 % Allowed : 23.03 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.29), residues: 805 helix: 1.83 (0.29), residues: 303 sheet: 0.24 (0.44), residues: 155 loop : -0.45 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.027 0.002 TYR A 541 PHE 0.013 0.001 PHE B 414 TRP 0.011 0.001 TRP B 257 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7335) covalent geometry : angle 0.57433 (10058) hydrogen bonds : bond 0.04690 ( 319) hydrogen bonds : angle 4.21466 ( 886) metal coordination : bond 0.00218 ( 4) metal coordination : angle 4.38471 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.188 Fit side-chains REVERT: A 283 LYS cc_start: 0.8616 (tppt) cc_final: 0.7961 (tttp) REVERT: A 387 MET cc_start: 0.9018 (mmp) cc_final: 0.8712 (mmt) REVERT: A 612 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 756 TYR cc_start: 0.7528 (t80) cc_final: 0.7140 (t80) REVERT: A 822 ASP cc_start: 0.8253 (m-30) cc_final: 0.7447 (t0) outliers start: 24 outliers final: 21 residues processed: 137 average time/residue: 0.0791 time to fit residues: 14.9297 Evaluate side-chains 142 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.159627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.125378 restraints weight = 8107.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.126307 restraints weight = 7771.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.127428 restraints weight = 6688.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.127635 restraints weight = 5100.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.128111 restraints weight = 4802.595| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7339 Z= 0.150 Angle : 0.579 7.813 10064 Z= 0.291 Chirality : 0.042 0.223 1164 Planarity : 0.003 0.041 1158 Dihedral : 15.956 165.226 1314 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.15 % Allowed : 23.18 % Favored : 73.68 % 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: 0.78 (0.29), residues: 805 helix: 1.83 (0.29), residues: 303 sheet: 0.22 (0.44), residues: 155 loop : -0.49 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 637 TYR 0.027 0.002 TYR A 541 PHE 0.010 0.001 PHE A 739 TRP 0.010 0.001 TRP B 257 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7335) covalent geometry : angle 0.57007 (10058) hydrogen bonds : bond 0.04622 ( 319) hydrogen bonds : angle 4.18253 ( 886) metal coordination : bond 0.00208 ( 4) metal coordination : angle 4.29704 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.259 Fit side-chains REVERT: A 283 LYS cc_start: 0.8619 (tppt) cc_final: 0.7936 (tttp) REVERT: A 387 MET cc_start: 0.9013 (mmp) cc_final: 0.8710 (mmt) REVERT: A 612 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 756 TYR cc_start: 0.7539 (t80) cc_final: 0.7135 (t80) REVERT: A 822 ASP cc_start: 0.8265 (m-30) cc_final: 0.7440 (t0) outliers start: 22 outliers final: 21 residues processed: 134 average time/residue: 0.0702 time to fit residues: 12.9611 Evaluate side-chains 142 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 ASN Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.164233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.129722 restraints weight = 8196.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.130456 restraints weight = 7565.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.131947 restraints weight = 6665.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.132371 restraints weight = 4825.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.132692 restraints weight = 4555.404| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7339 Z= 0.097 Angle : 0.548 9.138 10064 Z= 0.271 Chirality : 0.041 0.209 1164 Planarity : 0.003 0.040 1158 Dihedral : 15.962 164.506 1314 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.43 % Allowed : 24.18 % Favored : 73.39 % 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: 0.99 (0.30), residues: 805 helix: 2.02 (0.29), residues: 304 sheet: 0.45 (0.45), residues: 155 loop : -0.45 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.030 0.001 TYR A 541 PHE 0.013 0.001 PHE B 414 TRP 0.014 0.001 TRP B 257 HIS 0.003 0.001 HIS A 876 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 7335) covalent geometry : angle 0.54207 (10058) hydrogen bonds : bond 0.03795 ( 319) hydrogen bonds : angle 3.93589 ( 886) metal coordination : bond 0.00210 ( 4) metal coordination : angle 3.30275 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.224 Fit side-chains REVERT: A 283 LYS cc_start: 0.8571 (tppt) cc_final: 0.7957 (tttp) REVERT: A 387 MET cc_start: 0.8909 (mmp) cc_final: 0.8592 (mmt) REVERT: A 612 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7595 (tm-30) REVERT: A 652 LYS cc_start: 0.8222 (mttt) cc_final: 0.7906 (mttt) REVERT: A 756 TYR cc_start: 0.7534 (t80) cc_final: 0.7108 (t80) REVERT: A 822 ASP cc_start: 0.8239 (m-30) cc_final: 0.8020 (t70) outliers start: 17 outliers final: 16 residues processed: 134 average time/residue: 0.0812 time to fit residues: 14.6920 Evaluate side-chains 140 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 876 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.166785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.132223 restraints weight = 8174.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.132927 restraints weight = 7590.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.134430 restraints weight = 6593.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.135072 restraints weight = 4830.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.135359 restraints weight = 4510.443| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7339 Z= 0.095 Angle : 0.539 8.771 10064 Z= 0.267 Chirality : 0.040 0.208 1164 Planarity : 0.003 0.040 1158 Dihedral : 15.954 164.226 1314 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.58 % Allowed : 24.32 % Favored : 73.10 % 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: 1.05 (0.29), residues: 805 helix: 2.12 (0.29), residues: 304 sheet: 0.58 (0.46), residues: 145 loop : -0.49 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 342 TYR 0.029 0.001 TYR A 541 PHE 0.009 0.001 PHE A 911 TRP 0.013 0.001 TRP B 257 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 7335) covalent geometry : angle 0.53391 (10058) hydrogen bonds : bond 0.03592 ( 319) hydrogen bonds : angle 3.83535 ( 886) metal coordination : bond 0.00213 ( 4) metal coordination : angle 3.13754 ( 6) =============================================================================== Job complete usr+sys time: 1092.78 seconds wall clock time: 19 minutes 33.58 seconds (1173.58 seconds total)