Starting phenix.real_space_refine on Tue Jul 29 01:53:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jl1_22369/07_2025/7jl1_22369.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jl1_22369/07_2025/7jl1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2025/7jl1_22369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2025/7jl1_22369.map" model { file = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2025/7jl1_22369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jl1_22369/07_2025/7jl1_22369.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG: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: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} 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: 8.40, per 1000 atoms: 1.18 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: 4.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 4.87 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: 3.44 Time building geometry restraints manager: 3.86 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: 18.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 41.380 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.002 TRP B 315 HIS 0.020 0.002 HIS B 313 PHE 0.019 0.003 PHE A 295 TYR 0.031 0.003 TYR A 303 ARG 0.014 0.001 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.15475 ( 319) hydrogen bonds : angle 6.65900 ( 886) metal coordination : bond 0.00757 ( 4) metal coordination : angle 3.76063 ( 6) covalent geometry : bond 0.01072 ( 7335) covalent geometry : angle 1.38226 (10058) *********************** 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 : 2.030 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8411 (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: 0.8207 (t0) cc_final: 0.7863 (t0) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.4304 time to fit residues: 97.6564 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 : 2.203 ------------------------------------------------------------------------------- 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 70 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.157253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.124497 restraints weight = 8066.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.123300 restraints weight = 8096.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.125589 restraints weight = 8022.725| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7339 Z= 0.229 Angle : 0.692 7.948 10064 Z= 0.354 Chirality : 0.046 0.246 1164 Planarity : 0.004 0.040 1158 Dihedral : 16.390 163.755 1316 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.86 % Allowed : 13.30 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.29), residues: 805 helix: 1.25 (0.29), residues: 303 sheet: -0.03 (0.46), residues: 152 loop : -0.36 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 512 HIS 0.007 0.001 HIS A 782 PHE 0.017 0.002 PHE A 911 TYR 0.019 0.002 TYR A 541 ARG 0.005 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.06189 ( 319) hydrogen bonds : angle 5.06716 ( 886) metal coordination : bond 0.00358 ( 4) metal coordination : angle 5.11913 ( 6) covalent geometry : bond 0.00526 ( 7335) covalent geometry : angle 0.68078 (10058) *********************** 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 153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.887 Fit side-chains REVERT: A 283 LYS cc_start: 0.8589 (tppt) cc_final: 0.8205 (ttpt) REVERT: A 339 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6925 (mt-10) REVERT: A 387 MET cc_start: 0.9108 (mmp) cc_final: 0.8878 (mmt) REVERT: A 481 ASP cc_start: 0.8089 (m-30) cc_final: 0.7790 (m-30) REVERT: A 610 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7282 (mtpp) REVERT: A 657 LYS cc_start: 0.8744 (tptm) cc_final: 0.8481 (tptp) REVERT: A 692 ASN cc_start: 0.8357 (m-40) cc_final: 0.7743 (t0) REVERT: A 756 TYR cc_start: 0.7524 (t80) cc_final: 0.7283 (t80) REVERT: A 761 MET cc_start: 0.7434 (ttp) cc_final: 0.7155 (ttp) REVERT: A 822 ASP cc_start: 0.8459 (m-30) cc_final: 0.7762 (t0) REVERT: B 321 ASN cc_start: 0.8108 (t0) cc_final: 0.7867 (t0) REVERT: B 362 MET cc_start: 0.7656 (mmm) cc_final: 0.7032 (mtp) outliers start: 20 outliers final: 14 residues processed: 144 average time/residue: 0.3929 time to fit residues: 75.8040 Evaluate side-chains 138 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 894 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 271 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.159771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.126650 restraints weight = 8174.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.126619 restraints weight = 7960.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.127985 restraints weight = 8173.099| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7339 Z= 0.152 Angle : 0.596 6.877 10064 Z= 0.303 Chirality : 0.043 0.223 1164 Planarity : 0.004 0.042 1158 Dihedral : 16.206 165.644 1314 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.00 % Allowed : 17.88 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 805 helix: 1.51 (0.29), residues: 304 sheet: -0.01 (0.46), residues: 144 loop : -0.42 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 257 HIS 0.009 0.001 HIS A 876 PHE 0.014 0.001 PHE B 414 TYR 0.028 0.002 TYR A 541 ARG 0.003 0.000 ARG B 342 Details of bonding type rmsd hydrogen bonds : bond 0.05191 ( 319) hydrogen bonds : angle 4.59253 ( 886) metal coordination : bond 0.00218 ( 4) metal coordination : angle 4.39647 ( 6) covalent geometry : bond 0.00344 ( 7335) covalent geometry : angle 0.58604 (10058) *********************** 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 153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.860 Fit side-chains REVERT: A 283 LYS cc_start: 0.8591 (tppt) cc_final: 0.8039 (tttp) REVERT: A 387 MET cc_start: 0.9063 (mmp) cc_final: 0.8798 (mmt) REVERT: A 541 TYR cc_start: 0.7642 (m-80) cc_final: 0.7406 (m-80) REVERT: A 657 LYS cc_start: 0.8673 (tptm) cc_final: 0.8181 (tppt) REVERT: A 692 ASN cc_start: 0.8479 (m-40) cc_final: 0.7776 (t0) REVERT: A 756 TYR cc_start: 0.7464 (t80) cc_final: 0.7233 (t80) REVERT: A 761 MET cc_start: 0.7408 (ttp) cc_final: 0.7201 (ttp) REVERT: A 822 ASP cc_start: 0.8366 (m-30) cc_final: 0.7681 (t0) REVERT: B 321 ASN cc_start: 0.8086 (t0) cc_final: 0.7880 (t0) REVERT: B 362 MET cc_start: 0.7667 (mmm) cc_final: 0.7366 (ttm) outliers start: 21 outliers final: 18 residues processed: 142 average time/residue: 0.2542 time to fit residues: 48.7440 Evaluate side-chains 146 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 605 SER 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 826 ILE Chi-restraints excluded: chain A residue 833 VAL 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 339 VAL 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 75 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.160365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.126915 restraints weight = 8149.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.125813 restraints weight = 8054.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.127754 restraints weight = 8473.728| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7339 Z= 0.143 Angle : 0.574 7.186 10064 Z= 0.291 Chirality : 0.043 0.221 1164 Planarity : 0.003 0.042 1158 Dihedral : 16.172 165.214 1314 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.01 % Allowed : 19.74 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.30), residues: 805 helix: 1.63 (0.29), residues: 304 sheet: -0.11 (0.44), residues: 159 loop : -0.26 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 257 HIS 0.005 0.001 HIS B 260 PHE 0.012 0.001 PHE A 913 TYR 0.020 0.002 TYR A 541 ARG 0.002 0.000 ARG B 342 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 319) hydrogen bonds : angle 4.41051 ( 886) metal coordination : bond 0.00212 ( 4) metal coordination : angle 4.38288 ( 6) covalent geometry : bond 0.00323 ( 7335) covalent geometry : angle 0.56361 (10058) *********************** 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 169 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8620 (tppt) cc_final: 0.8034 (tttp) REVERT: A 387 MET cc_start: 0.9034 (mmp) cc_final: 0.8753 (mmt) REVERT: A 435 ASP cc_start: 0.8563 (t0) cc_final: 0.7948 (t0) REVERT: A 492 ASP cc_start: 0.8042 (p0) cc_final: 0.7807 (p0) REVERT: A 610 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7461 (mttt) REVERT: A 657 LYS cc_start: 0.8708 (tptm) cc_final: 0.8218 (tppt) REVERT: A 690 ASP cc_start: 0.8368 (p0) cc_final: 0.8050 (p0) REVERT: A 692 ASN cc_start: 0.8606 (m-40) cc_final: 0.7787 (t0) REVERT: A 756 TYR cc_start: 0.7527 (t80) cc_final: 0.7241 (t80) REVERT: A 822 ASP cc_start: 0.8356 (m-30) cc_final: 0.7673 (t0) REVERT: B 362 MET cc_start: 0.7761 (mmm) cc_final: 0.7516 (ttm) outliers start: 28 outliers final: 25 residues processed: 157 average time/residue: 0.1850 time to fit residues: 39.2337 Evaluate side-chains 159 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 762 ASN Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL 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 339 VAL 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 40 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 81 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 GLN A 782 HIS A 876 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.159584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.126116 restraints weight = 8080.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.125891 restraints weight = 8518.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.127206 restraints weight = 8611.624| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2365 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= 0.161 Angle : 0.583 7.623 10064 Z= 0.295 Chirality : 0.043 0.229 1164 Planarity : 0.003 0.042 1158 Dihedral : 16.153 165.500 1314 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.58 % Allowed : 20.17 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 805 helix: 1.63 (0.29), residues: 303 sheet: -0.15 (0.44), residues: 159 loop : -0.29 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 257 HIS 0.007 0.001 HIS A 782 PHE 0.013 0.001 PHE B 414 TYR 0.016 0.002 TYR A 303 ARG 0.002 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 319) hydrogen bonds : angle 4.41829 ( 886) metal coordination : bond 0.00209 ( 4) metal coordination : angle 4.46109 ( 6) covalent geometry : bond 0.00369 ( 7335) covalent geometry : angle 0.57277 (10058) *********************** 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 160 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.697 Fit side-chains REVERT: A 283 LYS cc_start: 0.8637 (tppt) cc_final: 0.8036 (tttp) REVERT: A 387 MET cc_start: 0.9058 (mmt) cc_final: 0.8765 (mmt) REVERT: A 554 ILE cc_start: 0.8947 (mm) cc_final: 0.8579 (mt) REVERT: A 657 LYS cc_start: 0.8664 (tptm) cc_final: 0.8180 (tppt) REVERT: A 756 TYR cc_start: 0.7541 (t80) cc_final: 0.7191 (t80) REVERT: A 822 ASP cc_start: 0.8356 (m-30) cc_final: 0.7615 (t0) REVERT: B 362 MET cc_start: 0.7787 (mmm) cc_final: 0.7574 (tpp) outliers start: 32 outliers final: 27 residues processed: 147 average time/residue: 0.1906 time to fit residues: 38.0097 Evaluate side-chains 153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL 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 762 ASN 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 833 VAL 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 339 VAL 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 31 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.155628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122738 restraints weight = 8153.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.121757 restraints weight = 8417.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.123525 restraints weight = 8288.779| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7339 Z= 0.255 Angle : 0.672 8.891 10064 Z= 0.342 Chirality : 0.046 0.267 1164 Planarity : 0.004 0.042 1158 Dihedral : 16.165 166.343 1314 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.86 % Allowed : 21.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 805 helix: 1.29 (0.28), residues: 305 sheet: -0.38 (0.43), residues: 157 loop : -0.57 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.013 0.001 HIS A 876 PHE 0.014 0.002 PHE A 911 TYR 0.022 0.002 TYR A 303 ARG 0.003 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.05975 ( 319) hydrogen bonds : angle 4.74018 ( 886) metal coordination : bond 0.00324 ( 4) metal coordination : angle 4.99740 ( 6) covalent geometry : bond 0.00593 ( 7335) covalent geometry : angle 0.66079 (10058) *********************** 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 156 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.733 Fit side-chains REVERT: A 283 LYS cc_start: 0.8698 (tppt) cc_final: 0.8184 (ttpp) REVERT: A 387 MET cc_start: 0.9160 (mmt) cc_final: 0.8919 (mmt) REVERT: A 657 LYS cc_start: 0.8676 (tptm) cc_final: 0.8192 (tppt) REVERT: A 756 TYR cc_start: 0.7570 (t80) cc_final: 0.7219 (t80) REVERT: A 822 ASP cc_start: 0.8331 (m-30) cc_final: 0.7661 (t0) REVERT: B 297 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: B 362 MET cc_start: 0.7761 (mmm) cc_final: 0.7560 (tpp) outliers start: 34 outliers final: 26 residues processed: 143 average time/residue: 0.1632 time to fit residues: 32.6532 Evaluate side-chains 145 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL 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 545 LEU 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 760 MET Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL 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 297 PHE Chi-restraints excluded: chain B residue 339 VAL 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 7 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.156688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.122750 restraints weight = 8065.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122759 restraints weight = 7948.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.124641 restraints weight = 8107.236| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7339 Z= 0.218 Angle : 0.652 8.654 10064 Z= 0.329 Chirality : 0.045 0.250 1164 Planarity : 0.004 0.041 1158 Dihedral : 16.116 166.158 1314 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.15 % Allowed : 23.46 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 805 helix: 1.34 (0.29), residues: 305 sheet: -0.39 (0.43), residues: 157 loop : -0.63 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.007 0.001 HIS A 876 PHE 0.014 0.002 PHE B 414 TYR 0.019 0.002 TYR A 303 ARG 0.002 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.05588 ( 319) hydrogen bonds : angle 4.65791 ( 886) metal coordination : bond 0.00287 ( 4) metal coordination : angle 4.84405 ( 6) covalent geometry : bond 0.00503 ( 7335) covalent geometry : angle 0.64168 (10058) *********************** 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 149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.692 Fit side-chains REVERT: A 283 LYS cc_start: 0.8626 (tppt) cc_final: 0.8133 (ttpp) REVERT: A 387 MET cc_start: 0.9098 (mmt) cc_final: 0.8860 (mmt) REVERT: A 657 LYS cc_start: 0.8602 (tptm) cc_final: 0.8109 (tppt) REVERT: A 756 TYR cc_start: 0.7586 (t80) cc_final: 0.7258 (t80) REVERT: A 822 ASP cc_start: 0.8362 (m-30) cc_final: 0.7659 (t0) outliers start: 29 outliers final: 25 residues processed: 138 average time/residue: 0.1877 time to fit residues: 35.5073 Evaluate side-chains 142 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL 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 545 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 674 THR 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 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL 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 259 ILE Chi-restraints excluded: chain B residue 339 VAL 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 75 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.156516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.123360 restraints weight = 8123.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.122391 restraints weight = 8456.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124223 restraints weight = 8220.154| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7339 Z= 0.205 Angle : 0.644 8.982 10064 Z= 0.325 Chirality : 0.044 0.246 1164 Planarity : 0.004 0.041 1158 Dihedral : 16.082 166.010 1314 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.72 % Allowed : 23.03 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 805 helix: 1.32 (0.29), residues: 306 sheet: -0.42 (0.43), residues: 157 loop : -0.61 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.004 0.001 HIS B 260 PHE 0.015 0.002 PHE A 911 TYR 0.019 0.002 TYR A 303 ARG 0.002 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.05454 ( 319) hydrogen bonds : angle 4.63803 ( 886) metal coordination : bond 0.00267 ( 4) metal coordination : angle 4.88152 ( 6) covalent geometry : bond 0.00475 ( 7335) covalent geometry : angle 0.63298 (10058) *********************** 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 155 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.685 Fit side-chains REVERT: A 283 LYS cc_start: 0.8631 (tppt) cc_final: 0.8130 (ttpp) REVERT: A 387 MET cc_start: 0.9131 (mmt) cc_final: 0.8908 (mmt) REVERT: A 504 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7910 (m-10) REVERT: A 657 LYS cc_start: 0.8592 (tptm) cc_final: 0.8105 (tppt) REVERT: A 756 TYR cc_start: 0.7578 (t80) cc_final: 0.7219 (t80) REVERT: A 822 ASP cc_start: 0.8342 (m-30) cc_final: 0.7652 (t0) REVERT: B 297 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7082 (m-80) outliers start: 33 outliers final: 26 residues processed: 145 average time/residue: 0.1918 time to fit residues: 38.2184 Evaluate side-chains 150 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL 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 504 PHE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 674 THR 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 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL 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 903 THR Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 339 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 25 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 0.0000 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.158844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.124052 restraints weight = 8278.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.125089 restraints weight = 7830.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.126289 restraints weight = 6518.900| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7339 Z= 0.151 Angle : 0.602 8.112 10064 Z= 0.302 Chirality : 0.043 0.225 1164 Planarity : 0.003 0.041 1158 Dihedral : 15.976 165.411 1314 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.29 % Allowed : 24.03 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 805 helix: 1.52 (0.29), residues: 303 sheet: -0.30 (0.43), residues: 157 loop : -0.53 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 315 HIS 0.004 0.001 HIS A 876 PHE 0.014 0.001 PHE B 414 TYR 0.029 0.002 TYR A 541 ARG 0.001 0.000 ARG B 342 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 319) hydrogen bonds : angle 4.44566 ( 886) metal coordination : bond 0.00203 ( 4) metal coordination : angle 4.37365 ( 6) covalent geometry : bond 0.00343 ( 7335) covalent geometry : angle 0.59219 (10058) *********************** 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 158 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.745 Fit side-chains REVERT: A 283 LYS cc_start: 0.8635 (tppt) cc_final: 0.7971 (tttp) REVERT: A 387 MET cc_start: 0.9072 (mmt) cc_final: 0.8841 (mmt) REVERT: A 521 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7370 (ttm) REVERT: A 657 LYS cc_start: 0.8612 (tptm) cc_final: 0.8106 (tppt) REVERT: A 756 TYR cc_start: 0.7488 (t80) cc_final: 0.7151 (t80) REVERT: A 822 ASP cc_start: 0.8361 (m-30) cc_final: 0.7573 (t0) REVERT: B 297 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.6989 (m-80) outliers start: 30 outliers final: 23 residues processed: 147 average time/residue: 0.1838 time to fit residues: 36.8214 Evaluate side-chains 151 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 521 MET Chi-restraints excluded: chain A residue 586 LEU 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 674 THR 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 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL 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 903 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 297 PHE 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 29 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.157823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.124283 restraints weight = 8212.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.125007 restraints weight = 7854.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.126341 restraints weight = 6990.904| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7339 Z= 0.169 Angle : 0.612 8.307 10064 Z= 0.308 Chirality : 0.043 0.232 1164 Planarity : 0.004 0.041 1158 Dihedral : 15.944 165.467 1314 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.15 % Allowed : 24.46 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.29), residues: 805 helix: 1.48 (0.29), residues: 303 sheet: -0.33 (0.43), residues: 157 loop : -0.56 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.004 0.001 HIS B 260 PHE 0.013 0.001 PHE A 911 TYR 0.028 0.002 TYR A 541 ARG 0.005 0.000 ARG A 859 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 319) hydrogen bonds : angle 4.46967 ( 886) metal coordination : bond 0.00219 ( 4) metal coordination : angle 4.46642 ( 6) covalent geometry : bond 0.00388 ( 7335) covalent geometry : angle 0.60263 (10058) ********************** 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 153 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.745 Fit side-chains REVERT: A 283 LYS cc_start: 0.8638 (tppt) cc_final: 0.7970 (tttp) REVERT: A 387 MET cc_start: 0.9080 (mmt) cc_final: 0.8841 (mmt) REVERT: A 521 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7359 (ttm) REVERT: A 657 LYS cc_start: 0.8608 (tptm) cc_final: 0.8105 (tppt) REVERT: A 756 TYR cc_start: 0.7489 (t80) cc_final: 0.7138 (t80) REVERT: A 822 ASP cc_start: 0.8329 (m-30) cc_final: 0.7517 (t0) REVERT: A 859 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7698 (tpt170) REVERT: B 297 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: B 392 VAL cc_start: 0.7825 (OUTLIER) cc_final: 0.7598 (p) outliers start: 29 outliers final: 24 residues processed: 142 average time/residue: 0.1898 time to fit residues: 36.4200 Evaluate side-chains 152 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL 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 521 MET Chi-restraints excluded: chain A residue 586 LEU 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 674 THR 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 826 ILE Chi-restraints excluded: chain A residue 829 CYS Chi-restraints excluded: chain A residue 833 VAL 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 903 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.158563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.123488 restraints weight = 8204.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.124409 restraints weight = 7772.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.125533 restraints weight = 6721.935| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7339 Z= 0.165 Angle : 0.609 8.439 10064 Z= 0.305 Chirality : 0.043 0.231 1164 Planarity : 0.003 0.041 1158 Dihedral : 15.939 165.443 1314 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.86 % Allowed : 24.89 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 805 helix: 1.50 (0.29), residues: 303 sheet: -0.24 (0.43), residues: 156 loop : -0.58 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.004 0.001 HIS B 260 PHE 0.013 0.001 PHE B 414 TYR 0.027 0.002 TYR A 541 ARG 0.002 0.000 ARG A 859 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 319) hydrogen bonds : angle 4.42073 ( 886) metal coordination : bond 0.00233 ( 4) metal coordination : angle 4.50902 ( 6) covalent geometry : bond 0.00378 ( 7335) covalent geometry : angle 0.59884 (10058) =============================================================================== Job complete usr+sys time: 2720.49 seconds wall clock time: 50 minutes 54.50 seconds (3054.50 seconds total)