Starting phenix.real_space_refine on Sun Jun 8 03:27:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtc_61794/06_2025/9jtc_61794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtc_61794/06_2025/9jtc_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_61794/06_2025/9jtc_61794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtc_61794/06_2025/9jtc_61794.map" model { file = "/net/cci-nas-00/data/ceres_data/9jtc_61794/06_2025/9jtc_61794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtc_61794/06_2025/9jtc_61794.cif" } resolution = 2.99 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 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.52, per 1000 atoms: 0.71 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.23 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: 3.24 Time building geometry restraints manager: 2.74 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=" C4' AMP C 201 " pdb=" O4' AMP C 201 " ideal model delta sigma weight residual 1.426 1.454 -0.028 2.00e-02 2.50e+03 1.95e+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=" C2' AMP C 201 " pdb=" O2' AMP C 201 " ideal model delta sigma weight residual 1.432 1.409 0.023 2.00e-02 2.50e+03 1.27e+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 ... (remaining 9369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12520 1.75 - 3.51: 176 3.51 - 5.26: 29 5.26 - 7.02: 8 7.02 - 8.77: 2 Bond angle restraints: 12735 Sorted by residual: angle pdb=" C1' AMP C 201 " pdb=" C2' AMP C 201 " pdb=" C3' AMP C 201 " ideal model delta sigma weight residual 111.00 102.23 8.77 3.00e+00 1.11e-01 8.55e+00 angle pdb=" C2' AMP C 201 " pdb=" C3' AMP C 201 " pdb=" C4' AMP C 201 " ideal model delta sigma weight residual 111.00 103.66 7.34 3.00e+00 1.11e-01 5.99e+00 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 ... (remaining 12730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5254 17.47 - 34.95: 278 34.95 - 52.42: 66 52.42 - 69.89: 32 69.89 - 87.37: 10 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 - 0.044: 1088 0.044 - 0.087: 256 0.087 - 0.131: 66 0.131 - 0.174: 4 0.174 - 0.218: 1 Chirality restraints: 1415 Sorted by residual: chirality pdb=" C3' AMP C 201 " pdb=" C2' AMP C 201 " pdb=" C4' AMP C 201 " pdb=" O3' AMP C 201 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.19e+00 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 ... (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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.190 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.850 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 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= 0.135 Angle : 0.557 8.773 12737 Z= 0.283 Chirality : 0.040 0.218 1415 Planarity : 0.004 0.047 1665 Dihedral : 13.024 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 (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: 0.75 (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 TRP 0.010 0.001 TRP A 385 HIS 0.005 0.001 HIS A 488 PHE 0.014 0.001 PHE A 541 TYR 0.012 0.002 TYR A 996 ARG 0.002 0.000 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.12584 ( 438) hydrogen bonds : angle 6.09289 ( 1209) SS BOND : bond 0.00681 ( 1) SS BOND : angle 1.38044 ( 2) covalent geometry : bond 0.00289 ( 9374) covalent geometry : angle 0.55701 (12735) Misc. bond : bond 0.00076 ( 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 : 0.936 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: 1.0702 time to fit residues: 159.7107 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 : 0.991 ------------------------------------------------------------------------------- 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 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 0.0770 chunk 90 optimal weight: 0.0270 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.1806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.195610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.161337 restraints weight = 12111.310| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.08 r_work: 0.3799 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9376 Z= 0.102 Angle : 0.516 6.518 12737 Z= 0.253 Chirality : 0.039 0.153 1415 Planarity : 0.004 0.043 1665 Dihedral : 5.024 47.783 1261 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.62 % Allowed : 9.61 % Favored : 88.78 % 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: 1.07 (0.25), residues: 1147 helix: 1.44 (0.24), residues: 453 sheet: 0.67 (0.40), residues: 155 loop : 0.20 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 903 HIS 0.005 0.001 HIS A 488 PHE 0.015 0.001 PHE A 541 TYR 0.010 0.001 TYR A 996 ARG 0.003 0.000 ARG A 544 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 438) hydrogen bonds : angle 4.83462 ( 1209) SS BOND : bond 0.00509 ( 1) SS BOND : angle 0.76387 ( 2) covalent geometry : bond 0.00226 ( 9374) covalent geometry : angle 0.51570 (12735) Misc. bond : bond 0.00051 ( 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 132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.407 Fit side-chains REVERT: A 54 MET cc_start: 0.5949 (ttm) cc_final: 0.5717 (ttm) REVERT: A 155 VAL cc_start: 0.7921 (t) cc_final: 0.7691 (p) REVERT: A 208 TRP cc_start: 0.6655 (m-10) cc_final: 0.6389 (m-10) REVERT: A 406 ASP cc_start: 0.6157 (t0) cc_final: 0.5913 (t0) REVERT: A 538 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6493 (mm) REVERT: A 541 PHE cc_start: 0.8201 (m-80) cc_final: 0.7995 (m-80) REVERT: A 685 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6680 (mm-40) REVERT: A 721 MET cc_start: 0.4162 (mpp) cc_final: 0.3938 (mpp) REVERT: A 898 PHE cc_start: 0.8007 (t80) cc_final: 0.7563 (t80) REVERT: A 983 GLU cc_start: 0.7821 (pp20) cc_final: 0.7479 (pm20) outliers start: 16 outliers final: 4 residues processed: 126 average time/residue: 1.4919 time to fit residues: 204.0498 Evaluate side-chains 117 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 572 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 94 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.194261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.160151 restraints weight = 12164.000| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.01 r_work: 0.3775 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1032 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= 0.134 Angle : 0.539 7.091 12737 Z= 0.261 Chirality : 0.040 0.213 1415 Planarity : 0.004 0.044 1665 Dihedral : 4.804 44.047 1259 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.02 % Allowed : 11.43 % Favored : 86.55 % 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: 0.89 (0.25), residues: 1147 helix: 1.40 (0.24), residues: 458 sheet: 0.37 (0.39), residues: 155 loop : 0.05 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 903 HIS 0.006 0.001 HIS A 290 PHE 0.012 0.001 PHE A 146 TYR 0.011 0.001 TYR A 996 ARG 0.007 0.000 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 438) hydrogen bonds : angle 4.69442 ( 1209) SS BOND : bond 0.00560 ( 1) SS BOND : angle 0.88253 ( 2) covalent geometry : bond 0.00313 ( 9374) covalent geometry : angle 0.53931 (12735) Misc. bond : bond 0.00005 ( 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 143 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.954 Fit side-chains REVERT: A 155 VAL cc_start: 0.7952 (t) cc_final: 0.7714 (p) REVERT: A 208 TRP cc_start: 0.6715 (m-10) cc_final: 0.6455 (m-10) REVERT: A 406 ASP cc_start: 0.6133 (t0) cc_final: 0.5917 (t0) REVERT: A 532 ASN cc_start: 0.8492 (m110) cc_final: 0.8138 (m110) REVERT: A 538 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6578 (mm) REVERT: A 685 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6751 (mm-40) REVERT: A 721 MET cc_start: 0.4183 (mpp) cc_final: 0.3920 (mpp) REVERT: A 860 LEU cc_start: 0.8175 (tp) cc_final: 0.7861 (tt) REVERT: A 898 PHE cc_start: 0.8073 (t80) cc_final: 0.7627 (t80) REVERT: A 983 GLU cc_start: 0.7775 (pp20) cc_final: 0.7404 (pm20) outliers start: 20 outliers final: 11 residues processed: 133 average time/residue: 1.5048 time to fit residues: 215.7249 Evaluate side-chains 132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 A residue 572 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 68 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.193195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158438 restraints weight = 12020.291| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.05 r_work: 0.3759 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9376 Z= 0.155 Angle : 0.554 8.834 12737 Z= 0.269 Chirality : 0.040 0.174 1415 Planarity : 0.004 0.045 1665 Dihedral : 4.860 43.893 1259 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.62 % Allowed : 12.74 % Favored : 85.64 % 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: 0.74 (0.25), residues: 1147 helix: 1.34 (0.24), residues: 459 sheet: 0.22 (0.39), residues: 157 loop : -0.07 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 903 HIS 0.006 0.001 HIS A 290 PHE 0.017 0.001 PHE A 425 TYR 0.012 0.002 TYR A 996 ARG 0.011 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 438) hydrogen bonds : angle 4.65820 ( 1209) SS BOND : bond 0.00575 ( 1) SS BOND : angle 0.94357 ( 2) covalent geometry : bond 0.00364 ( 9374) covalent geometry : angle 0.55431 (12735) Misc. bond : bond 0.00010 ( 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 145 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.889 Fit side-chains REVERT: A 208 TRP cc_start: 0.6651 (m-10) cc_final: 0.6393 (m-10) REVERT: A 406 ASP cc_start: 0.6189 (t0) cc_final: 0.5930 (t0) REVERT: A 468 MET cc_start: 0.6156 (tmm) cc_final: 0.5916 (tmm) REVERT: A 538 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6614 (mm) REVERT: A 580 ASN cc_start: 0.7448 (m-40) cc_final: 0.7162 (m110) REVERT: A 685 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6758 (mm-40) REVERT: A 721 MET cc_start: 0.4146 (mpp) cc_final: 0.3870 (mpp) REVERT: A 860 LEU cc_start: 0.8142 (tp) cc_final: 0.7909 (tp) REVERT: A 898 PHE cc_start: 0.8090 (t80) cc_final: 0.7609 (t80) REVERT: A 908 ARG cc_start: 0.8202 (ptp-170) cc_final: 0.7913 (ptp-170) REVERT: A 983 GLU cc_start: 0.7677 (pp20) cc_final: 0.7391 (pm20) REVERT: C 147 MET cc_start: 0.7692 (ptp) cc_final: 0.7482 (ptp) outliers start: 16 outliers final: 10 residues processed: 138 average time/residue: 1.0160 time to fit residues: 152.1593 Evaluate side-chains 134 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 61 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 0.0980 chunk 106 optimal weight: 0.4980 chunk 99 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 532 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4318 r_free = 0.4318 target = 0.193521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159473 restraints weight = 12131.048| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.01 r_work: 0.3785 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9376 Z= 0.116 Angle : 0.529 8.771 12737 Z= 0.254 Chirality : 0.039 0.220 1415 Planarity : 0.004 0.043 1665 Dihedral : 4.677 42.737 1259 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.92 % Allowed : 14.05 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.25), residues: 1147 helix: 1.48 (0.24), residues: 457 sheet: 0.23 (0.40), residues: 157 loop : -0.06 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 903 HIS 0.004 0.001 HIS A 290 PHE 0.009 0.001 PHE A 146 TYR 0.010 0.001 TYR A 996 ARG 0.008 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 438) hydrogen bonds : angle 4.54225 ( 1209) SS BOND : bond 0.00478 ( 1) SS BOND : angle 0.81160 ( 2) covalent geometry : bond 0.00268 ( 9374) covalent geometry : angle 0.52928 (12735) Misc. bond : bond 0.00001 ( 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 : 0.924 Fit side-chains REVERT: A 208 TRP cc_start: 0.6666 (m-10) cc_final: 0.6396 (m-10) REVERT: A 391 LEU cc_start: 0.7247 (mt) cc_final: 0.6568 (mp) REVERT: A 406 ASP cc_start: 0.6140 (t0) cc_final: 0.5902 (t0) REVERT: A 489 ARG cc_start: 0.6609 (ttp-170) cc_final: 0.5644 (mtp-110) REVERT: A 538 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6666 (mm) REVERT: A 580 ASN cc_start: 0.7417 (m-40) cc_final: 0.7204 (m110) REVERT: A 685 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6735 (mm-40) REVERT: A 721 MET cc_start: 0.4077 (mpp) cc_final: 0.3802 (mpp) REVERT: A 860 LEU cc_start: 0.8153 (tp) cc_final: 0.7908 (tp) REVERT: A 898 PHE cc_start: 0.8053 (t80) cc_final: 0.7689 (t80) REVERT: A 983 GLU cc_start: 0.7701 (pp20) cc_final: 0.7405 (pm20) outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 1.0964 time to fit residues: 165.8248 Evaluate side-chains 133 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 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 26 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 25 optimal weight: 0.0980 chunk 109 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 89 optimal weight: 0.2980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4333 r_free = 0.4333 target = 0.194884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.161447 restraints weight = 12037.776| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.97 r_work: 0.3808 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9376 Z= 0.097 Angle : 0.524 9.488 12737 Z= 0.249 Chirality : 0.039 0.272 1415 Planarity : 0.004 0.042 1665 Dihedral : 4.486 40.967 1259 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.62 % Allowed : 14.46 % Favored : 83.92 % 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: 0.99 (0.25), residues: 1147 helix: 1.60 (0.24), residues: 457 sheet: 0.30 (0.40), residues: 157 loop : 0.03 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 903 HIS 0.003 0.001 HIS A 290 PHE 0.014 0.001 PHE A 523 TYR 0.009 0.001 TYR A 996 ARG 0.008 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02793 ( 438) hydrogen bonds : angle 4.45079 ( 1209) SS BOND : bond 0.00393 ( 1) SS BOND : angle 0.61257 ( 2) covalent geometry : bond 0.00220 ( 9374) covalent geometry : angle 0.52439 (12735) Misc. bond : bond 0.00002 ( 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 145 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 208 TRP cc_start: 0.6672 (m-10) cc_final: 0.6395 (m-10) REVERT: A 406 ASP cc_start: 0.6045 (t0) cc_final: 0.5842 (t0) REVERT: A 489 ARG cc_start: 0.6615 (ttp-170) cc_final: 0.5609 (mtp-110) REVERT: A 563 THR cc_start: 0.8068 (p) cc_final: 0.7809 (p) REVERT: A 580 ASN cc_start: 0.7462 (m-40) cc_final: 0.7172 (m110) REVERT: A 582 LYS cc_start: 0.7303 (mptm) cc_final: 0.7065 (mptm) REVERT: A 685 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6748 (mm-40) REVERT: A 721 MET cc_start: 0.4040 (mpp) cc_final: 0.3766 (mpp) REVERT: A 898 PHE cc_start: 0.8041 (t80) cc_final: 0.7643 (t80) REVERT: A 983 GLU cc_start: 0.7701 (pp20) cc_final: 0.7411 (pm20) outliers start: 16 outliers final: 11 residues processed: 138 average time/residue: 1.0471 time to fit residues: 156.2968 Evaluate side-chains 138 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain A residue 382 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.192487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.158264 restraints weight = 12119.893| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.01 r_work: 0.3761 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9376 Z= 0.172 Angle : 0.586 11.992 12737 Z= 0.277 Chirality : 0.042 0.374 1415 Planarity : 0.004 0.043 1665 Dihedral : 4.648 38.957 1257 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.52 % Allowed : 15.07 % Favored : 83.42 % 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: 0.72 (0.25), residues: 1147 helix: 1.38 (0.24), residues: 458 sheet: 0.12 (0.39), residues: 157 loop : -0.12 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 903 HIS 0.007 0.001 HIS A 995 PHE 0.010 0.001 PHE A 146 TYR 0.013 0.002 TYR A 996 ARG 0.008 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 438) hydrogen bonds : angle 4.61732 ( 1209) SS BOND : bond 0.00563 ( 1) SS BOND : angle 1.05966 ( 2) covalent geometry : bond 0.00409 ( 9374) covalent geometry : angle 0.58559 (12735) Misc. bond : bond 0.00009 ( 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 142 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.855 Fit side-chains REVERT: A 208 TRP cc_start: 0.6676 (m-10) cc_final: 0.6425 (m-10) REVERT: A 406 ASP cc_start: 0.6198 (t0) cc_final: 0.5954 (t0) REVERT: A 489 ARG cc_start: 0.6601 (ttp-170) cc_final: 0.5722 (mtp-110) REVERT: A 580 ASN cc_start: 0.7492 (m-40) cc_final: 0.7173 (m110) REVERT: A 582 LYS cc_start: 0.7257 (mptm) cc_final: 0.6977 (mptm) REVERT: A 685 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6740 (mm-40) REVERT: A 721 MET cc_start: 0.3997 (mpp) cc_final: 0.3713 (mpp) REVERT: A 860 LEU cc_start: 0.8134 (tp) cc_final: 0.7856 (tt) REVERT: A 898 PHE cc_start: 0.8072 (t80) cc_final: 0.7647 (t80) REVERT: A 983 GLU cc_start: 0.7706 (pp20) cc_final: 0.7411 (pm20) outliers start: 15 outliers final: 13 residues processed: 136 average time/residue: 1.0325 time to fit residues: 152.0784 Evaluate side-chains 135 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 382 LEU 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 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 74 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 33 optimal weight: 0.2980 chunk 11 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 99 optimal weight: 0.1980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.195041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.161594 restraints weight = 12203.375| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.01 r_work: 0.3792 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9376 Z= 0.111 Angle : 0.549 12.406 12737 Z= 0.259 Chirality : 0.040 0.324 1415 Planarity : 0.004 0.043 1665 Dihedral : 4.476 38.830 1257 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.52 % Allowed : 15.67 % Favored : 82.81 % 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: 0.90 (0.25), residues: 1147 helix: 1.56 (0.24), residues: 458 sheet: 0.23 (0.40), residues: 157 loop : -0.05 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 903 HIS 0.004 0.001 HIS A 290 PHE 0.022 0.001 PHE A 425 TYR 0.010 0.001 TYR A 996 ARG 0.009 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02913 ( 438) hydrogen bonds : angle 4.49806 ( 1209) SS BOND : bond 0.00466 ( 1) SS BOND : angle 0.73509 ( 2) covalent geometry : bond 0.00257 ( 9374) covalent geometry : angle 0.54896 (12735) Misc. bond : bond 0.00002 ( 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 133 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.949 Fit side-chains REVERT: A 208 TRP cc_start: 0.6682 (m-10) cc_final: 0.6448 (m-10) REVERT: A 406 ASP cc_start: 0.6090 (t0) cc_final: 0.5857 (t0) REVERT: A 489 ARG cc_start: 0.6562 (ttp-170) cc_final: 0.5701 (mtp-110) REVERT: A 580 ASN cc_start: 0.7482 (m-40) cc_final: 0.7191 (m110) REVERT: A 582 LYS cc_start: 0.7281 (mptm) cc_final: 0.7024 (mptm) REVERT: A 685 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6767 (mm-40) REVERT: A 721 MET cc_start: 0.4055 (mpp) cc_final: 0.3755 (mpp) REVERT: A 860 LEU cc_start: 0.8155 (tp) cc_final: 0.7925 (tp) REVERT: A 898 PHE cc_start: 0.8079 (t80) cc_final: 0.7555 (t80) REVERT: A 983 GLU cc_start: 0.7761 (pp20) cc_final: 0.7472 (pm20) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 1.1097 time to fit residues: 152.6023 Evaluate side-chains 131 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 217 MET Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU 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 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 22 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 93 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.193761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.160335 restraints weight = 11944.765| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.97 r_work: 0.3777 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9376 Z= 0.156 Angle : 0.578 13.036 12737 Z= 0.274 Chirality : 0.041 0.338 1415 Planarity : 0.004 0.042 1665 Dihedral : 4.589 36.933 1257 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.02 % Allowed : 15.47 % Favored : 82.51 % 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: 0.76 (0.25), residues: 1147 helix: 1.42 (0.24), residues: 458 sheet: 0.18 (0.40), residues: 157 loop : -0.11 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 903 HIS 0.005 0.001 HIS A 995 PHE 0.013 0.001 PHE A 388 TYR 0.012 0.002 TYR A 996 ARG 0.010 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 438) hydrogen bonds : angle 4.57596 ( 1209) SS BOND : bond 0.00549 ( 1) SS BOND : angle 0.98110 ( 2) covalent geometry : bond 0.00368 ( 9374) covalent geometry : angle 0.57750 (12735) Misc. bond : bond 0.00010 ( 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 143 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.900 Fit side-chains REVERT: A 208 TRP cc_start: 0.6720 (m-10) cc_final: 0.6485 (m-10) REVERT: A 406 ASP cc_start: 0.6145 (t0) cc_final: 0.5896 (t0) REVERT: A 489 ARG cc_start: 0.6578 (ttp-170) cc_final: 0.5552 (mtp-110) REVERT: A 580 ASN cc_start: 0.7494 (m-40) cc_final: 0.7167 (m110) REVERT: A 582 LYS cc_start: 0.7268 (mptm) cc_final: 0.7015 (mptm) REVERT: A 685 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6804 (mm-40) REVERT: A 721 MET cc_start: 0.3936 (mpp) cc_final: 0.3653 (mpp) REVERT: A 860 LEU cc_start: 0.8152 (tp) cc_final: 0.7936 (tp) REVERT: A 898 PHE cc_start: 0.8084 (t80) cc_final: 0.7643 (t80) REVERT: A 983 GLU cc_start: 0.7727 (pp20) cc_final: 0.7428 (pm20) outliers start: 20 outliers final: 16 residues processed: 135 average time/residue: 1.0699 time to fit residues: 155.9821 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 : 1.002 ------------------------------------------------------------------------------- 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 470 HIS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 112 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 13 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.194731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.161246 restraints weight = 12173.770| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.01 r_work: 0.3788 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9376 Z= 0.119 Angle : 0.570 13.719 12737 Z= 0.269 Chirality : 0.040 0.318 1415 Planarity : 0.004 0.042 1665 Dihedral : 4.494 37.254 1257 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.62 % Allowed : 15.87 % Favored : 82.51 % 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: 0.84 (0.25), residues: 1147 helix: 1.49 (0.24), residues: 458 sheet: 0.23 (0.41), residues: 157 loop : -0.07 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 903 HIS 0.006 0.001 HIS A 142 PHE 0.017 0.001 PHE A 388 TYR 0.010 0.001 TYR A 996 ARG 0.010 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 438) hydrogen bonds : angle 4.50892 ( 1209) SS BOND : bond 0.00488 ( 1) SS BOND : angle 0.81185 ( 2) covalent geometry : bond 0.00277 ( 9374) covalent geometry : angle 0.56976 (12735) Misc. bond : bond 0.00001 ( 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 141 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.152 Fit side-chains REVERT: A 208 TRP cc_start: 0.6694 (m-10) cc_final: 0.6454 (m-10) REVERT: A 406 ASP cc_start: 0.6098 (t0) cc_final: 0.5843 (t0) REVERT: A 489 ARG cc_start: 0.6567 (ttp-170) cc_final: 0.5667 (mtp-110) REVERT: A 580 ASN cc_start: 0.7501 (m-40) cc_final: 0.7227 (m110) REVERT: A 582 LYS cc_start: 0.7262 (mptm) cc_final: 0.7020 (mptm) REVERT: A 685 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6809 (mm-40) REVERT: A 721 MET cc_start: 0.3960 (mpp) cc_final: 0.3670 (mpp) REVERT: A 860 LEU cc_start: 0.8146 (tp) cc_final: 0.7923 (tp) REVERT: A 898 PHE cc_start: 0.8085 (t80) cc_final: 0.7555 (t80) outliers start: 16 outliers final: 15 residues processed: 134 average time/residue: 1.1884 time to fit residues: 172.3120 Evaluate side-chains 136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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 470 HIS 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 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 41 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.193370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159641 restraints weight = 12057.074| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.99 r_work: 0.3777 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1910 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= 0.164 Angle : 0.595 13.659 12737 Z= 0.283 Chirality : 0.041 0.338 1415 Planarity : 0.004 0.042 1665 Dihedral : 4.580 36.453 1257 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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 (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: 0.73 (0.25), residues: 1147 helix: 1.40 (0.24), residues: 458 sheet: 0.16 (0.40), residues: 157 loop : -0.13 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 903 HIS 0.008 0.001 HIS A 142 PHE 0.027 0.002 PHE A 425 TYR 0.011 0.002 TYR A 996 ARG 0.010 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 438) hydrogen bonds : angle 4.58341 ( 1209) SS BOND : bond 0.00534 ( 1) SS BOND : angle 0.96224 ( 2) covalent geometry : bond 0.00390 ( 9374) covalent geometry : angle 0.59490 (12735) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8477.32 seconds wall clock time: 150 minutes 58.73 seconds (9058.73 seconds total)