Starting phenix.real_space_refine on Wed Aug 5 09:06:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtc_61794/08_2026/9jtc_61794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtc_61794/08_2026/9jtc_61794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jtc_61794/08_2026/9jtc_61794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtc_61794/08_2026/9jtc_61794.map" model { file = "/net/cci-nas-00/data/ceres_data/9jtc_61794/08_2026/9jtc_61794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtc_61794/08_2026/9jtc_61794.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 39 5.16 5 C 5806 2.51 5 N 1615 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9158 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7294 Classifications: {'peptide': 938} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 881} Chain breaks: 5 Chain: "B" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1232 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 15, 'TRANS': 134} Chain: "C" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 1.30, per 1000 atoms: 0.14 Number of scatterers: 9158 At special positions: 0 Unit cell: (80.352, 103.68, 112.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 1 15.00 O 1697 8.00 N 1615 7.00 C 5806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS B 86 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 309.6 milliseconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 46.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.583A pdb=" N LEU A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.528A pdb=" N LYS A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.545A pdb=" N LEU A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.571A pdb=" N ASN A 221 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 282 through 304 Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.581A pdb=" N MET A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 356 through 377 Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.942A pdb=" N VAL A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.636A pdb=" N GLN A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.744A pdb=" N GLU A 520 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 4.287A pdb=" N GLY A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 555 Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.590A pdb=" N VAL A 599 " --> pdb=" O PRO A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 622 Processing helix chain 'A' and resid 622 through 631 removed outlier: 3.752A pdb=" N LYS A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 637 through 645 removed outlier: 3.677A pdb=" N LYS A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 655 removed outlier: 3.571A pdb=" N LEU A 650 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 removed outlier: 4.561A pdb=" N LEU A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP A 670 " --> pdb=" O ASP A 666 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 671 " --> pdb=" O CYS A 667 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 719 through 738 Processing helix chain 'A' and resid 744 through 755 Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.777A pdb=" N LEU A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 774 removed outlier: 4.173A pdb=" N ASP A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 removed outlier: 3.805A pdb=" N GLN A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 825 removed outlier: 3.796A pdb=" N VAL A 813 " --> pdb=" O HIS A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 840 Processing helix chain 'A' and resid 845 through 865 removed outlier: 3.611A pdb=" N LYS A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 951 through 961 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.166A pdb=" N LEU B 48 " --> pdb=" O PRO B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 132 through 147 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.584A pdb=" N LEU C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.530A pdb=" N GLY C 138 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.613A pdb=" N VAL A 121 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 227 removed outlier: 6.717A pdb=" N ILE A 214 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLY A 250 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY A 251 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 193 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE A 184 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A 191 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 508 through 511 removed outlier: 6.704A pdb=" N VAL A 463 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU A 511 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 465 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 533 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 896 through 898 Processing sheet with id=AA6, first strand: chain 'A' and resid 908 through 912 removed outlier: 6.467A pdb=" N LEU A 909 " --> pdb=" O HIS A 995 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 997 " --> pdb=" O LEU A 909 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A 911 " --> pdb=" O LYS A 997 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS A 940 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU A 944 " --> pdb=" O HIS A 940 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 27 removed outlier: 5.460A pdb=" N ASN B 24 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 38 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 93 removed outlier: 4.636A pdb=" N LEU C 121 " --> pdb=" O MET C 128 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3074 1.34 - 1.46: 1791 1.46 - 1.58: 4451 1.58 - 1.69: 1 1.69 - 1.81: 57 Bond restraints: 9374 Sorted by residual: bond pdb=" C SER A 188 " pdb=" N PRO A 189 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.68e+00 bond pdb=" C ASP A 516 " pdb=" N PRO A 517 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.19e-02 7.06e+03 1.38e+00 bond pdb=" C SER B 56 " pdb=" N PHE B 57 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.61e-02 3.86e+03 1.05e+00 bond pdb=" CA ARG C 113 " pdb=" CB ARG C 113 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.61e-02 3.86e+03 7.38e-01 bond pdb=" CA VAL A 471 " pdb=" CB VAL A 471 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 6.63e-01 ... (remaining 9369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 12358 1.29 - 2.59: 288 2.59 - 3.88: 67 3.88 - 5.17: 14 5.17 - 6.46: 8 Bond angle restraints: 12735 Sorted by residual: angle pdb=" N ILE A 842 " pdb=" CA ILE A 842 " pdb=" C ILE A 842 " ideal model delta sigma weight residual 107.76 110.15 -2.39 1.01e+00 9.80e-01 5.61e+00 angle pdb=" N GLY A 354 " pdb=" CA GLY A 354 " pdb=" C GLY A 354 " ideal model delta sigma weight residual 111.57 115.63 -4.06 1.74e+00 3.30e-01 5.45e+00 angle pdb=" C ILE A 487 " pdb=" N HIS A 488 " pdb=" CA HIS A 488 " ideal model delta sigma weight residual 123.91 127.76 -3.85 1.66e+00 3.63e-01 5.37e+00 angle pdb=" C ALA A 353 " pdb=" N GLY A 354 " pdb=" CA GLY A 354 " ideal model delta sigma weight residual 122.47 120.43 2.04 8.90e-01 1.26e+00 5.25e+00 angle pdb=" C GLU B 28 " pdb=" N GLU B 29 " pdb=" CA GLU B 29 " ideal model delta sigma weight residual 121.54 125.91 -4.37 1.91e+00 2.74e-01 5.23e+00 ... (remaining 12730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5255 17.47 - 34.95: 277 34.95 - 52.42: 66 52.42 - 69.89: 31 69.89 - 87.37: 11 Dihedral angle restraints: 5640 sinusoidal: 2294 harmonic: 3346 Sorted by residual: dihedral pdb=" CA GLN A 915 " pdb=" C GLN A 915 " pdb=" N PRO A 916 " pdb=" CA PRO A 916 " ideal model delta harmonic sigma weight residual 180.00 154.41 25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PRO A 189 " pdb=" C PRO A 189 " pdb=" N GLY A 190 " pdb=" CA GLY A 190 " ideal model delta harmonic sigma weight residual 180.00 -159.22 -20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA THR A 563 " pdb=" C THR A 563 " pdb=" N MET A 564 " pdb=" CA MET A 564 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 5637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 877 0.030 - 0.060: 374 0.060 - 0.091: 105 0.091 - 0.121: 52 0.121 - 0.151: 7 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA HIS A 488 " pdb=" N HIS A 488 " pdb=" C HIS A 488 " pdb=" CB HIS A 488 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CB ILE A 602 " pdb=" CA ILE A 602 " pdb=" CG1 ILE A 602 " pdb=" CG2 ILE A 602 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE A 574 " pdb=" N ILE A 574 " pdb=" C ILE A 574 " pdb=" CB ILE A 574 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1412 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 516 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 517 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 43 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B 44 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 759 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 760 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " 0.017 5.00e-02 4.00e+02 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 5594 3.05 - 3.51: 9461 3.51 - 3.97: 14509 3.97 - 4.44: 17716 4.44 - 4.90: 27698 Nonbonded interactions: 74978 Sorted by model distance: nonbonded pdb=" C GLY C 154 " pdb=" O1P AMP C 201 " model vdw 2.583 2.616 nonbonded pdb=" N ASP A 516 " pdb=" O ASP A 516 " model vdw 2.596 2.496 nonbonded pdb=" O GLN B 128 " pdb=" OD1 ASP B 132 " model vdw 2.614 3.040 nonbonded pdb=" O SER A 188 " pdb=" C PRO A 189 " model vdw 2.619 3.270 nonbonded pdb=" O THR A 241 " pdb=" OG1 THR A 241 " model vdw 2.621 3.040 ... (remaining 74973 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.310 Find NCS groups from input model: 0.020 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:5.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 : 0.003 0.038 9376 Z= 0.133 Angle : 0.542 6.463 12737 Z= 0.280 Chirality : 0.040 0.151 1415 Planarity : 0.004 0.047 1665 Dihedral : 13.039 87.369 3471 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.91 % Allowed : 5.97 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1147 helix: 0.98 (0.24), residues: 455 sheet: 0.76 (0.40), residues: 155 loop : 0.12 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 654 TYR 0.012 0.002 TYR A 996 PHE 0.014 0.001 PHE A 541 TRP 0.010 0.001 TRP A 385 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9374) covalent geometry : angle 0.54169 / 0.28 (12735) SS BOND : bond 0.00681 / 0.36 ( 1) SS BOND : angle 1.38044 / 0.80 ( 2) hydrogen bonds : bond 0.12584 / 8.33 ( 438) hydrogen bonds : angle 6.09289 / 4.51 ( 1209) Misc. bond : bond 0.00076 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.257 Fit side-chains REVERT: A 54 MET cc_start: 0.5870 (ttm) cc_final: 0.5596 (ttm) REVERT: A 208 TRP cc_start: 0.6527 (m-10) cc_final: 0.6285 (m-10) REVERT: A 392 ASP cc_start: 0.7765 (p0) cc_final: 0.7518 (p0) REVERT: A 538 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6432 (mm) REVERT: A 721 MET cc_start: 0.4613 (mpp) cc_final: 0.4350 (mpp) REVERT: A 754 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.6032 (mm) REVERT: A 761 GLN cc_start: 0.6613 (mm-40) cc_final: 0.6267 (mm-40) REVERT: A 860 LEU cc_start: 0.8190 (tp) cc_final: 0.7889 (tp) REVERT: A 898 PHE cc_start: 0.8021 (t80) cc_final: 0.7615 (t80) outliers start: 9 outliers final: 1 residues processed: 138 average time/residue: 0.3895 time to fit residues: 58.1423 Evaluate side-chains 125 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 754 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS A 926 HIS B 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.191909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157272 restraints weight = 12122.907| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.06 r_work: 0.3739 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9376 Z= 0.224 Angle : 0.611 6.831 12737 Z= 0.304 Chirality : 0.043 0.150 1415 Planarity : 0.005 0.051 1665 Dihedral : 5.814 60.382 1261 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.02 % Allowed : 10.31 % Favored : 87.66 % 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: 0.40 (0.25), residues: 1147 helix: 0.85 (0.23), residues: 460 sheet: 0.33 (0.39), residues: 155 loop : -0.16 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 544 TYR 0.015 0.002 TYR C 93 PHE 0.017 0.002 PHE A 425 TRP 0.016 0.002 TRP A 385 HIS 0.009 0.001 HIS A 995 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 ( 9374) covalent geometry : angle 0.61070 / 0.30 (12735) SS BOND : bond 0.00737 / 0.39 ( 1) SS BOND : angle 1.17419 / 0.68 ( 2) hydrogen bonds : bond 0.04030 / 2.63 ( 438) hydrogen bonds : angle 5.06953 / 3.71 ( 1209) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.278 Fit side-chains REVERT: A 208 TRP cc_start: 0.6680 (m-10) cc_final: 0.6443 (m-10) REVERT: A 406 ASP cc_start: 0.6259 (t0) cc_final: 0.6008 (t0) REVERT: A 468 MET cc_start: 0.6371 (tmm) cc_final: 0.6065 (tmm) REVERT: A 489 ARG cc_start: 0.6620 (ttp-170) cc_final: 0.6356 (ttp-170) REVERT: A 538 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6497 (mm) REVERT: A 580 ASN cc_start: 0.7414 (m-40) cc_final: 0.7109 (m110) REVERT: A 685 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6753 (mm-40) REVERT: A 721 MET cc_start: 0.4238 (mpp) cc_final: 0.3990 (mpp) REVERT: A 898 PHE cc_start: 0.8128 (t80) cc_final: 0.7613 (t80) REVERT: A 983 GLU cc_start: 0.7774 (pp20) cc_final: 0.7442 (pm20) outliers start: 20 outliers final: 7 residues processed: 131 average time/residue: 0.3857 time to fit residues: 54.7141 Evaluate side-chains 127 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain B residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 24 optimal weight: 0.0050 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 105 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 532 ASN A 931 GLN B 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.192355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158428 restraints weight = 12126.225| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.99 r_work: 0.3760 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9376 Z= 0.147 Angle : 0.532 6.419 12737 Z= 0.263 Chirality : 0.040 0.147 1415 Planarity : 0.004 0.047 1665 Dihedral : 5.400 61.146 1259 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.42 % Allowed : 12.84 % Favored : 85.74 % 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: 0.57 (0.25), residues: 1147 helix: 1.15 (0.24), residues: 458 sheet: 0.19 (0.39), residues: 155 loop : -0.15 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 934 TYR 0.012 0.002 TYR A 996 PHE 0.012 0.001 PHE A 146 TRP 0.012 0.001 TRP A 903 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9374) covalent geometry : angle 0.53231 / 0.26 (12735) SS BOND : bond 0.00603 / 0.32 ( 1) SS BOND : angle 0.97524 / 0.55 ( 2) hydrogen bonds : bond 0.03379 / 2.20 ( 438) hydrogen bonds : angle 4.77754 / 3.49 ( 1209) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.289 Fit side-chains REVERT: A 208 TRP cc_start: 0.6712 (m-10) cc_final: 0.6469 (m-10) REVERT: A 406 ASP cc_start: 0.6242 (t0) cc_final: 0.5960 (t0) REVERT: A 468 MET cc_start: 0.6454 (tmm) cc_final: 0.6252 (tmm) REVERT: A 538 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6539 (mm) REVERT: A 580 ASN cc_start: 0.7405 (m-40) cc_final: 0.7161 (m110) REVERT: A 685 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6768 (mm-40) REVERT: A 721 MET cc_start: 0.4296 (mpp) cc_final: 0.4003 (mpp) REVERT: A 860 LEU cc_start: 0.8159 (tp) cc_final: 0.7921 (tp) REVERT: A 898 PHE cc_start: 0.8101 (t80) cc_final: 0.7654 (t80) REVERT: A 982 TYR cc_start: 0.8393 (m-80) cc_final: 0.8073 (m-80) REVERT: A 983 GLU cc_start: 0.7732 (pp20) cc_final: 0.7422 (pm20) outliers start: 14 outliers final: 6 residues processed: 136 average time/residue: 0.4030 time to fit residues: 59.4040 Evaluate side-chains 130 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 88 optimal weight: 0.0970 chunk 109 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 931 GLN B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.192838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.158751 restraints weight = 12161.711| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.00 r_work: 0.3772 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9376 Z= 0.126 Angle : 0.512 6.823 12737 Z= 0.253 Chirality : 0.039 0.136 1415 Planarity : 0.004 0.044 1665 Dihedral : 5.232 58.907 1259 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.12 % Allowed : 12.94 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1147 helix: 1.30 (0.24), residues: 460 sheet: 0.16 (0.39), residues: 155 loop : -0.13 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 287 TYR 0.012 0.001 TYR A 996 PHE 0.011 0.001 PHE A 388 TRP 0.014 0.001 TRP A 903 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9374) covalent geometry : angle 0.51163 / 0.25 (12735) SS BOND : bond 0.00508 / 0.27 ( 1) SS BOND : angle 0.87931 / 0.50 ( 2) hydrogen bonds : bond 0.03111 / 2.02 ( 438) hydrogen bonds : angle 4.62638 / 3.37 ( 1209) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 208 TRP cc_start: 0.6677 (m-10) cc_final: 0.6439 (m-10) REVERT: A 406 ASP cc_start: 0.6184 (t0) cc_final: 0.5905 (t0) REVERT: A 468 MET cc_start: 0.6431 (tmm) cc_final: 0.6199 (tmm) REVERT: A 538 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6438 (mt) REVERT: A 580 ASN cc_start: 0.7401 (m-40) cc_final: 0.7156 (m110) REVERT: A 685 GLN cc_start: 0.7189 (mm-40) cc_final: 0.6722 (mm-40) REVERT: A 721 MET cc_start: 0.4192 (mpp) cc_final: 0.3919 (mpp) REVERT: A 754 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6136 (mm) REVERT: A 898 PHE cc_start: 0.8067 (t80) cc_final: 0.7624 (t80) REVERT: A 983 GLU cc_start: 0.7673 (pp20) cc_final: 0.7364 (pm20) outliers start: 21 outliers final: 12 residues processed: 139 average time/residue: 0.3933 time to fit residues: 59.3223 Evaluate side-chains 135 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 75 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.192441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157657 restraints weight = 12057.817| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.04 r_work: 0.3753 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9376 Z= 0.163 Angle : 0.551 8.983 12737 Z= 0.269 Chirality : 0.041 0.215 1415 Planarity : 0.004 0.045 1665 Dihedral : 5.258 53.544 1259 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.92 % Allowed : 13.35 % Favored : 84.73 % 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: 0.57 (0.25), residues: 1147 helix: 1.21 (0.24), residues: 460 sheet: 0.09 (0.39), residues: 155 loop : -0.18 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 287 TYR 0.013 0.002 TYR A 996 PHE 0.011 0.001 PHE A 146 TRP 0.018 0.002 TRP A 903 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 9374) covalent geometry : angle 0.55080 / 0.27 (12735) SS BOND : bond 0.00571 / 0.30 ( 1) SS BOND : angle 1.03139 / 0.59 ( 2) hydrogen bonds : bond 0.03334 / 2.15 ( 438) hydrogen bonds : angle 4.68675 / 3.42 ( 1209) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 208 TRP cc_start: 0.6664 (m-10) cc_final: 0.6431 (m-10) REVERT: A 406 ASP cc_start: 0.6225 (t0) cc_final: 0.5951 (t0) REVERT: A 468 MET cc_start: 0.6479 (tmm) cc_final: 0.6216 (tmm) REVERT: A 538 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6464 (mt) REVERT: A 580 ASN cc_start: 0.7444 (m-40) cc_final: 0.7169 (m110) REVERT: A 685 GLN cc_start: 0.7192 (mm-40) cc_final: 0.6751 (mm-40) REVERT: A 721 MET cc_start: 0.4150 (mpp) cc_final: 0.3899 (mpp) REVERT: A 754 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6146 (mm) REVERT: A 860 LEU cc_start: 0.8129 (tp) cc_final: 0.7889 (tp) REVERT: A 898 PHE cc_start: 0.8089 (t80) cc_final: 0.7630 (t80) REVERT: A 983 GLU cc_start: 0.7688 (pp20) cc_final: 0.7388 (pm20) outliers start: 19 outliers final: 16 residues processed: 140 average time/residue: 0.4141 time to fit residues: 62.4738 Evaluate side-chains 141 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.191686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157427 restraints weight = 12160.502| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.01 r_work: 0.3752 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9376 Z= 0.175 Angle : 0.550 7.435 12737 Z= 0.270 Chirality : 0.041 0.170 1415 Planarity : 0.004 0.045 1665 Dihedral : 5.263 52.139 1259 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.12 % Allowed : 14.86 % Favored : 83.01 % 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: 0.50 (0.25), residues: 1147 helix: 1.18 (0.24), residues: 460 sheet: 0.02 (0.39), residues: 155 loop : -0.22 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 287 TYR 0.013 0.002 TYR A 996 PHE 0.014 0.001 PHE A 523 TRP 0.019 0.002 TRP A 903 HIS 0.006 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 9374) covalent geometry : angle 0.54994 / 0.27 (12735) SS BOND : bond 0.00611 / 0.32 ( 1) SS BOND : angle 1.05792 / 0.61 ( 2) hydrogen bonds : bond 0.03378 / 2.18 ( 438) hydrogen bonds : angle 4.70725 / 3.44 ( 1209) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 208 TRP cc_start: 0.6707 (m-10) cc_final: 0.6456 (m-10) REVERT: A 391 LEU cc_start: 0.7333 (mt) cc_final: 0.6651 (mp) REVERT: A 406 ASP cc_start: 0.6225 (t0) cc_final: 0.5949 (t0) REVERT: A 468 MET cc_start: 0.6472 (tmm) cc_final: 0.6205 (tmm) REVERT: A 538 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6446 (mt) REVERT: A 580 ASN cc_start: 0.7420 (m-40) cc_final: 0.7146 (m110) REVERT: A 685 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6748 (mm-40) REVERT: A 721 MET cc_start: 0.4179 (mpp) cc_final: 0.3922 (mpp) REVERT: A 754 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6182 (mm) REVERT: A 860 LEU cc_start: 0.8150 (tp) cc_final: 0.7905 (tp) REVERT: A 898 PHE cc_start: 0.8094 (t80) cc_final: 0.7640 (t80) REVERT: A 983 GLU cc_start: 0.7670 (pp20) cc_final: 0.7366 (pm20) outliers start: 21 outliers final: 14 residues processed: 141 average time/residue: 0.4218 time to fit residues: 64.1257 Evaluate side-chains 140 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.192605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158466 restraints weight = 12074.772| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.00 r_work: 0.3765 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9376 Z= 0.134 Angle : 0.528 7.591 12737 Z= 0.258 Chirality : 0.039 0.147 1415 Planarity : 0.004 0.045 1665 Dihedral : 5.158 54.436 1259 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.43 % Allowed : 14.66 % Favored : 82.91 % 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: 0.62 (0.25), residues: 1147 helix: 1.33 (0.24), residues: 458 sheet: 0.09 (0.40), residues: 155 loop : -0.21 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 287 TYR 0.012 0.001 TYR A 996 PHE 0.014 0.001 PHE A 293 TRP 0.022 0.001 TRP A 903 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 9374) covalent geometry : angle 0.52783 / 0.26 (12735) SS BOND : bond 0.00539 / 0.28 ( 1) SS BOND : angle 0.90621 / 0.52 ( 2) hydrogen bonds : bond 0.03126 / 2.01 ( 438) hydrogen bonds : angle 4.59148 / 3.35 ( 1209) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 208 TRP cc_start: 0.6704 (m-10) cc_final: 0.6468 (m-10) REVERT: A 406 ASP cc_start: 0.6200 (t0) cc_final: 0.5942 (t0) REVERT: A 468 MET cc_start: 0.6439 (tmm) cc_final: 0.6153 (tmm) REVERT: A 538 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6411 (mt) REVERT: A 580 ASN cc_start: 0.7418 (m-40) cc_final: 0.7161 (m110) REVERT: A 647 GLN cc_start: 0.5797 (OUTLIER) cc_final: 0.5543 (mm-40) REVERT: A 685 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6738 (mm-40) REVERT: A 721 MET cc_start: 0.4170 (mpp) cc_final: 0.3894 (mpp) REVERT: A 754 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6184 (mm) REVERT: A 860 LEU cc_start: 0.8131 (tp) cc_final: 0.7874 (tp) REVERT: A 898 PHE cc_start: 0.8101 (t80) cc_final: 0.7661 (t80) REVERT: A 983 GLU cc_start: 0.7647 (pp20) cc_final: 0.7332 (pm20) outliers start: 24 outliers final: 15 residues processed: 145 average time/residue: 0.3834 time to fit residues: 60.2770 Evaluate side-chains 144 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 23 optimal weight: 0.0770 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.0040 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 81 optimal weight: 0.5980 chunk 106 optimal weight: 0.4980 overall best weight: 0.2550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.194097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.160441 restraints weight = 12001.053| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.97 r_work: 0.3794 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9376 Z= 0.107 Angle : 0.510 7.425 12737 Z= 0.249 Chirality : 0.039 0.144 1415 Planarity : 0.004 0.053 1665 Dihedral : 5.024 56.741 1259 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.43 % Allowed : 15.17 % Favored : 82.41 % 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: 0.78 (0.25), residues: 1147 helix: 1.46 (0.24), residues: 458 sheet: 0.21 (0.40), residues: 155 loop : -0.14 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 934 TYR 0.011 0.001 TYR A 996 PHE 0.012 0.001 PHE A 388 TRP 0.023 0.001 TRP A 903 HIS 0.004 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9374) covalent geometry : angle 0.50952 / 0.25 (12735) SS BOND : bond 0.00453 / 0.24 ( 1) SS BOND : angle 0.71429 / 0.41 ( 2) hydrogen bonds : bond 0.02924 / 1.87 ( 438) hydrogen bonds : angle 4.49534 / 3.29 ( 1209) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 155 VAL cc_start: 0.7963 (t) cc_final: 0.7758 (p) REVERT: A 208 TRP cc_start: 0.6736 (m-10) cc_final: 0.6478 (m-10) REVERT: A 293 PHE cc_start: 0.7888 (m-80) cc_final: 0.7640 (m-80) REVERT: A 406 ASP cc_start: 0.6095 (t0) cc_final: 0.5872 (t0) REVERT: A 468 MET cc_start: 0.6488 (tmm) cc_final: 0.6234 (tmm) REVERT: A 563 THR cc_start: 0.8058 (p) cc_final: 0.7764 (p) REVERT: A 580 ASN cc_start: 0.7445 (m-40) cc_final: 0.7197 (m110) REVERT: A 647 GLN cc_start: 0.5799 (OUTLIER) cc_final: 0.5555 (mm-40) REVERT: A 685 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6803 (mm-40) REVERT: A 721 MET cc_start: 0.4124 (mpp) cc_final: 0.3846 (mpp) REVERT: A 754 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6224 (mm) REVERT: A 860 LEU cc_start: 0.8150 (tp) cc_final: 0.7876 (tp) REVERT: A 898 PHE cc_start: 0.8085 (t80) cc_final: 0.7703 (t80) outliers start: 24 outliers final: 14 residues processed: 147 average time/residue: 0.4117 time to fit residues: 65.6995 Evaluate side-chains 143 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 899 HIS B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.192010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.157943 restraints weight = 11992.333| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.97 r_work: 0.3761 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9376 Z= 0.193 Angle : 0.578 8.003 12737 Z= 0.284 Chirality : 0.041 0.143 1415 Planarity : 0.004 0.048 1665 Dihedral : 5.131 49.820 1257 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.82 % Allowed : 15.77 % Favored : 82.41 % 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: 0.53 (0.25), residues: 1147 helix: 1.21 (0.24), residues: 460 sheet: 0.05 (0.40), residues: 155 loop : -0.24 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 934 TYR 0.014 0.002 TYR A 733 PHE 0.015 0.002 PHE A 388 TRP 0.023 0.002 TRP A 903 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 9374) covalent geometry : angle 0.57784 / 0.28 (12735) SS BOND : bond 0.00608 / 0.32 ( 1) SS BOND : angle 1.17618 / 0.68 ( 2) hydrogen bonds : bond 0.03460 / 2.23 ( 438) hydrogen bonds : angle 4.67477 / 3.42 ( 1209) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.330 Fit side-chains REVERT: A 208 TRP cc_start: 0.6743 (m-10) cc_final: 0.6492 (m-10) REVERT: A 406 ASP cc_start: 0.6186 (t0) cc_final: 0.5895 (t0) REVERT: A 468 MET cc_start: 0.6516 (tmm) cc_final: 0.6264 (tmm) REVERT: A 489 ARG cc_start: 0.6664 (ttp-170) cc_final: 0.6412 (ttp-170) REVERT: A 580 ASN cc_start: 0.7498 (m-40) cc_final: 0.7192 (m110) REVERT: A 582 LYS cc_start: 0.7281 (mptm) cc_final: 0.7033 (mptm) REVERT: A 685 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6795 (mm-40) REVERT: A 721 MET cc_start: 0.4163 (mpp) cc_final: 0.3874 (mpp) REVERT: A 754 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6241 (mm) REVERT: A 898 PHE cc_start: 0.8072 (t80) cc_final: 0.7712 (t80) outliers start: 18 outliers final: 16 residues processed: 140 average time/residue: 0.4145 time to fit residues: 62.8171 Evaluate side-chains 142 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 8.9990 chunk 9 optimal weight: 0.0170 chunk 17 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 112 optimal weight: 0.0970 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 512 ASN B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.193366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159738 restraints weight = 12019.384| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.99 r_work: 0.3780 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9376 Z= 0.130 Angle : 0.541 8.103 12737 Z= 0.264 Chirality : 0.039 0.151 1415 Planarity : 0.004 0.044 1665 Dihedral : 5.010 53.247 1257 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.02 % Allowed : 15.98 % Favored : 82.00 % 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: 0.63 (0.25), residues: 1147 helix: 1.32 (0.24), residues: 458 sheet: 0.13 (0.40), residues: 155 loop : -0.19 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 934 TYR 0.019 0.002 TYR A 434 PHE 0.019 0.001 PHE A 388 TRP 0.025 0.001 TRP A 903 HIS 0.005 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9374) covalent geometry : angle 0.54140 / 0.26 (12735) SS BOND : bond 0.00538 / 0.28 ( 1) SS BOND : angle 0.88147 / 0.50 ( 2) hydrogen bonds : bond 0.03119 / 1.99 ( 438) hydrogen bonds : angle 4.57121 / 3.35 ( 1209) Misc. bond : bond 0.00004 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.326 Fit side-chains REVERT: A 208 TRP cc_start: 0.6755 (m-10) cc_final: 0.6507 (m-10) REVERT: A 406 ASP cc_start: 0.6109 (t0) cc_final: 0.5830 (t0) REVERT: A 468 MET cc_start: 0.6462 (tmm) cc_final: 0.6190 (tmm) REVERT: A 489 ARG cc_start: 0.6665 (ttp-170) cc_final: 0.6414 (ttp-170) REVERT: A 580 ASN cc_start: 0.7413 (m-40) cc_final: 0.7130 (m110) REVERT: A 582 LYS cc_start: 0.7281 (mptm) cc_final: 0.7013 (mptm) REVERT: A 685 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6800 (mm-40) REVERT: A 721 MET cc_start: 0.4191 (mpp) cc_final: 0.3887 (mpp) REVERT: A 754 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6214 (mm) REVERT: A 898 PHE cc_start: 0.8086 (t80) cc_final: 0.7727 (t80) outliers start: 20 outliers final: 15 residues processed: 142 average time/residue: 0.3868 time to fit residues: 59.7377 Evaluate side-chains 138 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 512 ASN A 899 HIS B 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.192501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158597 restraints weight = 11995.724| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.97 r_work: 0.3770 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9376 Z= 0.167 Angle : 0.571 7.782 12737 Z= 0.280 Chirality : 0.041 0.143 1415 Planarity : 0.004 0.045 1665 Dihedral : 5.085 51.483 1257 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.72 % Allowed : 16.08 % Favored : 82.20 % 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: 0.54 (0.25), residues: 1147 helix: 1.22 (0.24), residues: 458 sheet: 0.12 (0.40), residues: 155 loop : -0.24 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 934 TYR 0.016 0.002 TYR A 434 PHE 0.019 0.001 PHE A 388 TRP 0.023 0.002 TRP A 903 HIS 0.007 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 9374) covalent geometry : angle 0.57051 / 0.28 (12735) SS BOND : bond 0.00566 / 0.30 ( 1) SS BOND : angle 1.05580 / 0.61 ( 2) hydrogen bonds : bond 0.03344 / 2.14 ( 438) hydrogen bonds : angle 4.64045 / 3.39 ( 1209) Misc. bond : bond 0.00008 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2839.21 seconds wall clock time: 49 minutes 2.61 seconds (2942.61 seconds total)