Starting phenix.real_space_refine on Wed Apr 30 05:07:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtc_61794/04_2025/9jtc_61794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtc_61794/04_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_61794/04_2025/9jtc_61794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtc_61794/04_2025/9jtc_61794.map" model { file = "/net/cci-nas-00/data/ceres_data/9jtc_61794/04_2025/9jtc_61794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtc_61794/04_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-5669/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 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 6.37, per 1000 atoms: 0.70 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 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: 1.05 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: 3.19 Time building geometry restraints manager: 2.67 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: 15 5.17 - 6.46: 7 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 73.280 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.360 Find NCS groups from input model: 0.110 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.270 ------------------------------------------------------------------------------- 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= 0.133 Angle : 0.541 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 (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 0.00284 ( 9374) covalent geometry : angle 0.54119 (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 : 0.959 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: 1.0732 time to fit residues: 160.2094 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 : 1.085 ------------------------------------------------------------------------------- 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: B 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.195581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.161313 restraints weight = 12120.864| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.08 r_work: 0.3798 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.0739 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= 0.103 Angle : 0.509 6.488 12737 Z= 0.252 Chirality : 0.038 0.153 1415 Planarity : 0.004 0.043 1665 Dihedral : 5.493 73.699 1261 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.72 % Allowed : 9.50 % 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 0.012 0.001 TRP A 903 HIS 0.005 0.001 HIS A 488 PHE 0.014 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 0.03326 ( 438) hydrogen bonds : angle 4.84785 ( 1209) SS BOND : bond 0.00518 ( 1) SS BOND : angle 0.78034 ( 2) covalent geometry : bond 0.00227 ( 9374) covalent geometry : angle 0.50873 (12735) Misc. bond : bond 0.00003 ( 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 133 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.191 Fit side-chains REVERT: A 54 MET cc_start: 0.5954 (ttm) cc_final: 0.5721 (ttm) REVERT: A 155 VAL cc_start: 0.7926 (t) cc_final: 0.7699 (p) REVERT: A 208 TRP cc_start: 0.6666 (m-10) cc_final: 0.6399 (m-10) REVERT: A 406 ASP cc_start: 0.6162 (t0) cc_final: 0.5920 (t0) REVERT: A 538 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6479 (mm) REVERT: A 541 PHE cc_start: 0.8190 (m-80) cc_final: 0.7977 (m-80) REVERT: A 685 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6668 (mm-40) REVERT: A 721 MET cc_start: 0.4182 (mpp) cc_final: 0.3957 (mpp) REVERT: A 898 PHE cc_start: 0.8009 (t80) cc_final: 0.7564 (t80) REVERT: A 983 GLU cc_start: 0.7802 (pp20) cc_final: 0.7466 (pm20) outliers start: 17 outliers final: 4 residues processed: 126 average time/residue: 1.2762 time to fit residues: 174.3847 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 : 1.246 ------------------------------------------------------------------------------- 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: 0.0980 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 111 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.194121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159922 restraints weight = 12157.270| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.02 r_work: 0.3773 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1057 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= 0.136 Angle : 0.536 6.978 12737 Z= 0.261 Chirality : 0.040 0.209 1415 Planarity : 0.004 0.044 1665 Dihedral : 5.278 64.819 1259 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.12 % Allowed : 11.32 % 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: 0.87 (0.25), residues: 1147 helix: 1.38 (0.24), residues: 458 sheet: 0.36 (0.39), residues: 155 loop : 0.04 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 903 HIS 0.006 0.001 HIS A 290 PHE 0.012 0.001 PHE A 146 TYR 0.012 0.002 TYR A 996 ARG 0.008 0.000 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 438) hydrogen bonds : angle 4.68858 ( 1209) SS BOND : bond 0.00551 ( 1) SS BOND : angle 0.88824 ( 2) covalent geometry : bond 0.00317 ( 9374) covalent geometry : angle 0.53589 (12735) Misc. bond : bond 0.00001 ( 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 148 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.982 Fit side-chains REVERT: A 208 TRP cc_start: 0.6746 (m-10) cc_final: 0.6481 (m-10) REVERT: A 406 ASP cc_start: 0.6131 (t0) cc_final: 0.5907 (t0) REVERT: A 532 ASN cc_start: 0.8490 (m110) cc_final: 0.8143 (m110) REVERT: A 538 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6578 (mm) REVERT: A 685 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6754 (mm-40) REVERT: A 721 MET cc_start: 0.4152 (mpp) cc_final: 0.3889 (mpp) REVERT: A 860 LEU cc_start: 0.8176 (tp) cc_final: 0.7911 (tp) REVERT: A 898 PHE cc_start: 0.8073 (t80) cc_final: 0.7629 (t80) REVERT: A 983 GLU cc_start: 0.7763 (pp20) cc_final: 0.7411 (pm20) outliers start: 21 outliers final: 10 residues processed: 137 average time/residue: 1.1958 time to fit residues: 178.0175 Evaluate side-chains 135 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 13 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.193248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159208 restraints weight = 12060.468| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.01 r_work: 0.3767 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1294 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= 0.147 Angle : 0.543 9.815 12737 Z= 0.264 Chirality : 0.041 0.352 1415 Planarity : 0.004 0.044 1665 Dihedral : 5.243 58.840 1259 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.62 % Allowed : 12.84 % Favored : 85.54 % 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: 0.80 (0.25), residues: 1147 helix: 1.38 (0.24), residues: 459 sheet: 0.31 (0.40), residues: 157 loop : -0.06 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 903 HIS 0.006 0.001 HIS A 290 PHE 0.017 0.001 PHE A 425 TYR 0.011 0.002 TYR B 61 ARG 0.010 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 438) hydrogen bonds : angle 4.64070 ( 1209) SS BOND : bond 0.00549 ( 1) SS BOND : angle 0.92263 ( 2) covalent geometry : bond 0.00346 ( 9374) covalent geometry : angle 0.54261 (12735) Misc. bond : bond 0.00003 ( 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: 16 poor density : 132 time to evaluate : 1.087 Fit side-chains REVERT: A 208 TRP cc_start: 0.6689 (m-10) cc_final: 0.6418 (m-10) REVERT: A 406 ASP cc_start: 0.6154 (t0) cc_final: 0.5904 (t0) REVERT: A 468 MET cc_start: 0.6139 (tmm) cc_final: 0.5900 (tmm) REVERT: A 489 ARG cc_start: 0.6682 (ttp-170) cc_final: 0.6468 (ttp-170) REVERT: A 538 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6613 (mm) REVERT: A 580 ASN cc_start: 0.7520 (m110) cc_final: 0.7257 (m-40) REVERT: A 685 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6772 (mm-40) REVERT: A 721 MET cc_start: 0.4157 (mpp) cc_final: 0.3877 (mpp) REVERT: A 860 LEU cc_start: 0.8151 (tp) cc_final: 0.7915 (tp) REVERT: A 898 PHE cc_start: 0.8099 (t80) cc_final: 0.7593 (t80) REVERT: A 983 GLU cc_start: 0.7792 (pp20) cc_final: 0.7508 (pm20) outliers start: 16 outliers final: 9 residues processed: 141 average time/residue: 1.3422 time to fit residues: 205.1710 Evaluate side-chains 139 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 27 optimal weight: 0.3980 chunk 61 optimal weight: 0.4980 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 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 50 ASN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4307 r_free = 0.4307 target = 0.193070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158331 restraints weight = 12058.424| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.04 r_work: 0.3763 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9376 Z= 0.156 Angle : 0.550 8.881 12737 Z= 0.268 Chirality : 0.041 0.296 1415 Planarity : 0.004 0.044 1665 Dihedral : 5.223 55.309 1259 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.22 % Allowed : 13.14 % Favored : 84.63 % 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: 0.70 (0.25), residues: 1147 helix: 1.33 (0.24), residues: 459 sheet: 0.23 (0.40), residues: 157 loop : -0.14 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 903 HIS 0.006 0.001 HIS A 290 PHE 0.011 0.001 PHE A 146 TYR 0.012 0.002 TYR A 996 ARG 0.006 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 438) hydrogen bonds : angle 4.63337 ( 1209) SS BOND : bond 0.00553 ( 1) SS BOND : angle 0.98807 ( 2) covalent geometry : bond 0.00369 ( 9374) covalent geometry : angle 0.55035 (12735) Misc. bond : bond 0.00007 ( 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 147 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.259 Fit side-chains REVERT: A 208 TRP cc_start: 0.6658 (m-10) cc_final: 0.6398 (m-10) REVERT: A 406 ASP cc_start: 0.6247 (t0) cc_final: 0.5979 (t0) REVERT: A 538 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6648 (mm) REVERT: A 685 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6778 (mm-40) REVERT: A 721 MET cc_start: 0.4075 (mpp) cc_final: 0.3801 (mpp) REVERT: A 898 PHE cc_start: 0.8078 (t80) cc_final: 0.7656 (t80) REVERT: A 983 GLU cc_start: 0.7721 (pp20) cc_final: 0.7425 (pm20) outliers start: 22 outliers final: 15 residues processed: 137 average time/residue: 1.0789 time to fit residues: 160.2171 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 : 1.073 ------------------------------------------------------------------------------- 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 147 LEU 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 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 904 THR 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: 0.6980 chunk 73 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 38 optimal weight: 0.4980 chunk 25 optimal weight: 0.1980 chunk 109 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 470 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.194417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.160978 restraints weight = 12041.088| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.99 r_work: 0.3786 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9376 Z= 0.119 Angle : 0.532 10.199 12737 Z= 0.256 Chirality : 0.039 0.226 1415 Planarity : 0.004 0.043 1665 Dihedral : 5.093 56.678 1259 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.02 % Allowed : 13.85 % Favored : 84.13 % 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: 0.79 (0.25), residues: 1147 helix: 1.44 (0.24), residues: 457 sheet: 0.24 (0.41), residues: 157 loop : -0.10 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 903 HIS 0.004 0.001 HIS A 290 PHE 0.013 0.001 PHE A 523 TYR 0.011 0.001 TYR A 996 ARG 0.010 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 438) hydrogen bonds : angle 4.53640 ( 1209) SS BOND : bond 0.00474 ( 1) SS BOND : angle 0.84285 ( 2) covalent geometry : bond 0.00275 ( 9374) covalent geometry : angle 0.53232 (12735) Misc. bond : bond 0.00001 ( 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: 20 poor density : 129 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 208 TRP cc_start: 0.6653 (m-10) cc_final: 0.6404 (m-10) REVERT: A 406 ASP cc_start: 0.6135 (t0) cc_final: 0.5884 (t0) REVERT: A 538 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6414 (mt) REVERT: A 685 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6755 (mm-40) REVERT: A 721 MET cc_start: 0.4115 (mpp) cc_final: 0.3820 (mpp) REVERT: A 860 LEU cc_start: 0.8170 (tp) cc_final: 0.7884 (tp) REVERT: A 898 PHE cc_start: 0.8081 (t80) cc_final: 0.7551 (t80) REVERT: A 983 GLU cc_start: 0.7755 (pp20) cc_final: 0.7474 (pm20) outliers start: 20 outliers final: 15 residues processed: 139 average time/residue: 1.0263 time to fit residues: 154.9293 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 : 1.035 ------------------------------------------------------------------------------- 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 147 LEU 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 487 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 597 CYS 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 25 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 59 optimal weight: 0.0000 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 overall best weight: 0.1782 ------------------------------------------------------------------------------- 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** B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.195782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162706 restraints weight = 12145.216| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.99 r_work: 0.3802 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1680 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 : 0.526 11.546 12737 Z= 0.251 Chirality : 0.039 0.287 1415 Planarity : 0.004 0.043 1665 Dihedral : 4.954 58.900 1259 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.82 % Allowed : 14.96 % Favored : 83.22 % 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: 0.97 (0.25), residues: 1147 helix: 1.63 (0.24), residues: 457 sheet: 0.33 (0.41), residues: 157 loop : -0.04 (0.28), 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 958 PHE 0.013 0.001 PHE A 523 TYR 0.009 0.001 TYR A 996 ARG 0.007 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02755 ( 438) hydrogen bonds : angle 4.42961 ( 1209) SS BOND : bond 0.00396 ( 1) SS BOND : angle 0.58308 ( 2) covalent geometry : bond 0.00218 ( 9374) covalent geometry : angle 0.52631 (12735) Misc. bond : bond 0.00007 ( 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 149 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 208 TRP cc_start: 0.6653 (m-10) cc_final: 0.6415 (m-10) REVERT: A 406 ASP cc_start: 0.6003 (t0) cc_final: 0.5790 (t0) REVERT: A 538 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6435 (mt) REVERT: A 685 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6772 (mm-40) REVERT: A 721 MET cc_start: 0.4028 (mpp) cc_final: 0.3731 (mpp) REVERT: A 860 LEU cc_start: 0.8157 (tp) cc_final: 0.7846 (tp) REVERT: A 898 PHE cc_start: 0.8068 (t80) cc_final: 0.7580 (t80) outliers start: 18 outliers final: 14 residues processed: 139 average time/residue: 1.0311 time to fit residues: 155.9349 Evaluate side-chains 138 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 147 LEU 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 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 574 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 99 optimal weight: 0.0270 overall best weight: 0.5640 ------------------------------------------------------------------------------- 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 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 = 0.4319 r_free = 0.4319 target = 0.193790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.160256 restraints weight = 12206.647| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.00 r_work: 0.3775 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1773 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= 0.160 Angle : 0.564 12.402 12737 Z= 0.272 Chirality : 0.041 0.305 1415 Planarity : 0.004 0.043 1665 Dihedral : 5.046 52.076 1259 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.63 % Allowed : 14.36 % 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 (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: 0.79 (0.25), residues: 1147 helix: 1.46 (0.24), residues: 458 sheet: 0.18 (0.40), residues: 157 loop : -0.11 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 903 HIS 0.005 0.001 HIS A 290 PHE 0.010 0.001 PHE A 388 TYR 0.012 0.002 TYR A 996 ARG 0.009 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 438) hydrogen bonds : angle 4.54577 ( 1209) SS BOND : bond 0.00511 ( 1) SS BOND : angle 0.94312 ( 2) covalent geometry : bond 0.00377 ( 9374) covalent geometry : angle 0.56380 (12735) Misc. bond : bond 0.00006 ( 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 150 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.148 Fit side-chains REVERT: A 208 TRP cc_start: 0.6702 (m-10) cc_final: 0.6474 (m-10) REVERT: A 406 ASP cc_start: 0.6114 (t0) cc_final: 0.5893 (t0) REVERT: A 685 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6790 (mm-40) REVERT: A 721 MET cc_start: 0.4014 (mpp) cc_final: 0.3723 (mpp) REVERT: A 898 PHE cc_start: 0.8081 (t80) cc_final: 0.7704 (t80) REVERT: A 983 GLU cc_start: 0.7677 (pp20) cc_final: 0.7341 (pm20) outliers start: 26 outliers final: 17 residues processed: 140 average time/residue: 1.0484 time to fit residues: 159.6571 Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 147 LEU 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 574 ILE Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 904 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A 899 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 = 0.4298 r_free = 0.4298 target = 0.191823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157662 restraints weight = 11935.630| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.99 r_work: 0.3751 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9376 Z= 0.207 Angle : 0.612 13.389 12737 Z= 0.297 Chirality : 0.043 0.381 1415 Planarity : 0.004 0.043 1665 Dihedral : 5.174 48.275 1257 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.12 % Allowed : 14.76 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1147 helix: 1.17 (0.24), residues: 458 sheet: 0.06 (0.40), residues: 157 loop : -0.25 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 903 HIS 0.006 0.001 HIS A 290 PHE 0.026 0.002 PHE A 425 TYR 0.017 0.002 TYR A 434 ARG 0.011 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 438) hydrogen bonds : angle 4.71911 ( 1209) SS BOND : bond 0.00628 ( 1) SS BOND : angle 1.27147 ( 2) covalent geometry : bond 0.00492 ( 9374) covalent geometry : angle 0.61215 (12735) Misc. bond : bond 0.00012 ( 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 146 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.077 Fit side-chains REVERT: A 208 TRP cc_start: 0.6680 (m-10) cc_final: 0.6451 (m-10) REVERT: A 391 LEU cc_start: 0.7310 (mt) cc_final: 0.7003 (mp) REVERT: A 406 ASP cc_start: 0.6198 (t0) cc_final: 0.5928 (t0) REVERT: A 685 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6771 (mm-40) REVERT: A 721 MET cc_start: 0.4050 (mpp) cc_final: 0.3754 (mpp) REVERT: A 898 PHE cc_start: 0.8053 (t80) cc_final: 0.7622 (t80) REVERT: A 983 GLU cc_start: 0.7618 (pp20) cc_final: 0.7299 (pm20) outliers start: 21 outliers final: 14 residues processed: 136 average time/residue: 1.0873 time to fit residues: 160.0804 Evaluate side-chains 136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 217 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 0.0170 chunk 100 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN ** 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 = 0.4312 r_free = 0.4312 target = 0.193022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159253 restraints weight = 12147.121| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.99 r_work: 0.3774 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1940 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= 0.158 Angle : 0.586 13.542 12737 Z= 0.282 Chirality : 0.041 0.369 1415 Planarity : 0.004 0.043 1665 Dihedral : 5.088 52.081 1257 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.02 % Allowed : 15.17 % 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: 0.56 (0.25), residues: 1147 helix: 1.23 (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 TRP 0.026 0.002 TRP A 903 HIS 0.006 0.001 HIS A 290 PHE 0.021 0.001 PHE A 425 TYR 0.014 0.002 TYR A 434 ARG 0.010 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 438) hydrogen bonds : angle 4.62771 ( 1209) SS BOND : bond 0.00566 ( 1) SS BOND : angle 0.99349 ( 2) covalent geometry : bond 0.00374 ( 9374) covalent geometry : angle 0.58543 (12735) Misc. bond : bond 0.00008 ( 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 142 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.903 Fit side-chains REVERT: A 208 TRP cc_start: 0.6716 (m-10) cc_final: 0.6472 (m-10) REVERT: A 391 LEU cc_start: 0.7231 (mt) cc_final: 0.6940 (mp) REVERT: A 406 ASP cc_start: 0.6160 (t0) cc_final: 0.5872 (t0) REVERT: A 685 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6792 (mm-40) REVERT: A 721 MET cc_start: 0.3958 (mpp) cc_final: 0.3675 (mpp) REVERT: A 898 PHE cc_start: 0.8089 (t80) cc_final: 0.7613 (t80) REVERT: A 983 GLU cc_start: 0.7626 (pp20) cc_final: 0.7309 (pm20) outliers start: 20 outliers final: 16 residues processed: 131 average time/residue: 1.2149 time to fit residues: 171.9033 Evaluate side-chains 134 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 177 LEU Chi-restraints excluded: chain A residue 217 MET 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 487 ILE Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 140 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 77 optimal weight: 30.0000 chunk 98 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 470 HIS A 512 ASN A 580 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 HIS B 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.192754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.159024 restraints weight = 12063.236| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.99 r_work: 0.3765 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9376 Z= 0.181 Angle : 0.608 13.593 12737 Z= 0.293 Chirality : 0.042 0.386 1415 Planarity : 0.004 0.043 1665 Dihedral : 5.134 51.509 1257 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.92 % Allowed : 15.47 % Favored : 82.61 % 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: 0.46 (0.25), residues: 1147 helix: 1.12 (0.24), residues: 458 sheet: 0.00 (0.39), residues: 155 loop : -0.23 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 903 HIS 0.007 0.001 HIS A 142 PHE 0.021 0.002 PHE A 425 TYR 0.013 0.002 TYR A 434 ARG 0.010 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 438) hydrogen bonds : angle 4.66201 ( 1209) SS BOND : bond 0.00594 ( 1) SS BOND : angle 1.10556 ( 2) covalent geometry : bond 0.00430 ( 9374) covalent geometry : angle 0.60807 (12735) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8101.33 seconds wall clock time: 142 minutes 41.57 seconds (8561.57 seconds total)