Starting phenix.real_space_refine on Wed Sep 17 14:52:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtc_61794/09_2025/9jtc_61794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtc_61794/09_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_61794/09_2025/9jtc_61794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtc_61794/09_2025/9jtc_61794.map" model { file = "/net/cci-nas-00/data/ceres_data/9jtc_61794/09_2025/9jtc_61794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtc_61794/09_2025/9jtc_61794.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 39 5.16 5 C 5806 2.51 5 N 1615 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9158 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7294 Classifications: {'peptide': 938} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 881} Chain breaks: 5 Chain: "B" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1232 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 15, 'TRANS': 134} Chain: "C" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.24 Number of scatterers: 9158 At special positions: 0 Unit cell: (80.352, 103.68, 112.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 1 15.00 O 1697 8.00 N 1615 7.00 C 5806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS B 86 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 347.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 46.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.583A pdb=" N LEU A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.528A pdb=" N LYS A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.545A pdb=" N LEU A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.571A pdb=" N ASN A 221 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 282 through 304 Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.581A pdb=" N MET A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 356 through 377 Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.942A pdb=" N VAL A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.636A pdb=" N GLN A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.744A pdb=" N GLU A 520 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 4.287A pdb=" N GLY A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 555 Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.590A pdb=" N VAL A 599 " --> pdb=" O PRO A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 622 Processing helix chain 'A' and resid 622 through 631 removed outlier: 3.752A pdb=" N LYS A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 637 through 645 removed outlier: 3.677A pdb=" N LYS A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 655 removed outlier: 3.571A pdb=" N LEU A 650 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 removed outlier: 4.561A pdb=" N LEU A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP A 670 " --> pdb=" O ASP A 666 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 671 " --> pdb=" O CYS A 667 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 719 through 738 Processing helix chain 'A' and resid 744 through 755 Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.777A pdb=" N LEU A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 774 removed outlier: 4.173A pdb=" N ASP A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 removed outlier: 3.805A pdb=" N GLN A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 825 removed outlier: 3.796A pdb=" N VAL A 813 " --> pdb=" O HIS A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 840 Processing helix chain 'A' and resid 845 through 865 removed outlier: 3.611A pdb=" N LYS A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 951 through 961 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.166A pdb=" N LEU B 48 " --> pdb=" O PRO B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 132 through 147 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.584A pdb=" N LEU C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.530A pdb=" N GLY C 138 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.613A pdb=" N VAL A 121 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 227 removed outlier: 6.717A pdb=" N ILE A 214 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLY A 250 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY A 251 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 193 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE A 184 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A 191 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 508 through 511 removed outlier: 6.704A pdb=" N VAL A 463 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU A 511 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 465 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 533 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 896 through 898 Processing sheet with id=AA6, first strand: chain 'A' and resid 908 through 912 removed outlier: 6.467A pdb=" N LEU A 909 " --> pdb=" O HIS A 995 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 997 " --> pdb=" O LEU A 909 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A 911 " --> pdb=" O LYS A 997 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS A 940 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU A 944 " --> pdb=" O HIS A 940 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 27 removed outlier: 5.460A pdb=" N ASN B 24 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 38 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 93 removed outlier: 4.636A pdb=" N LEU C 121 " --> pdb=" O MET C 128 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.11 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: 5.360 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.25), residues: 1147 helix: 0.98 (0.24), residues: 455 sheet: 0.76 (0.40), residues: 155 loop : 0.12 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 654 TYR 0.012 0.002 TYR A 996 PHE 0.014 0.001 PHE A 541 TRP 0.010 0.001 TRP A 385 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9374) covalent geometry : angle 0.55701 (12735) SS BOND : bond 0.00681 ( 1) SS BOND : angle 1.38044 ( 2) hydrogen bonds : bond 0.12584 ( 438) hydrogen bonds : angle 6.09289 ( 1209) 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 : 0.268 Fit side-chains REVERT: A 54 MET cc_start: 0.5870 (ttm) cc_final: 0.5596 (ttm) REVERT: A 208 TRP cc_start: 0.6527 (m-10) cc_final: 0.6285 (m-10) REVERT: A 392 ASP cc_start: 0.7765 (p0) cc_final: 0.7518 (p0) REVERT: A 538 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6432 (mm) REVERT: A 721 MET cc_start: 0.4613 (mpp) cc_final: 0.4350 (mpp) REVERT: A 754 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.6032 (mm) REVERT: A 761 GLN cc_start: 0.6613 (mm-40) cc_final: 0.6267 (mm-40) REVERT: A 860 LEU cc_start: 0.8190 (tp) cc_final: 0.7889 (tp) REVERT: A 898 PHE cc_start: 0.8021 (t80) cc_final: 0.7615 (t80) outliers start: 9 outliers final: 1 residues processed: 138 average time/residue: 0.5185 time to fit residues: 76.9695 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 : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 754 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS A 926 HIS B 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.191924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157240 restraints weight = 12121.275| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.06 r_work: 0.3738 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9376 Z= 0.224 Angle : 0.616 6.801 12737 Z= 0.304 Chirality : 0.043 0.150 1415 Planarity : 0.005 0.050 1665 Dihedral : 5.464 47.307 1261 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.02 % Allowed : 10.31 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.25), residues: 1147 helix: 0.84 (0.23), residues: 460 sheet: 0.32 (0.39), residues: 155 loop : -0.16 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 544 TYR 0.015 0.002 TYR C 93 PHE 0.016 0.002 PHE A 425 TRP 0.016 0.002 TRP A 385 HIS 0.009 0.001 HIS A 995 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 9374) covalent geometry : angle 0.61602 (12735) SS BOND : bond 0.00736 ( 1) SS BOND : angle 1.14620 ( 2) hydrogen bonds : bond 0.04026 ( 438) hydrogen bonds : angle 5.06393 ( 1209) Misc. bond : bond 0.00056 ( 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 140 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.375 Fit side-chains REVERT: A 208 TRP cc_start: 0.6679 (m-10) cc_final: 0.6442 (m-10) REVERT: A 406 ASP cc_start: 0.6266 (t0) cc_final: 0.6015 (t0) REVERT: A 468 MET cc_start: 0.6392 (tmm) cc_final: 0.6089 (tmm) REVERT: A 489 ARG cc_start: 0.6624 (ttp-170) cc_final: 0.6401 (ttp-170) REVERT: A 538 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6498 (mm) REVERT: A 580 ASN cc_start: 0.7418 (m-40) cc_final: 0.7113 (m110) REVERT: A 685 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6752 (mm-40) REVERT: A 721 MET cc_start: 0.4242 (mpp) cc_final: 0.3992 (mpp) REVERT: A 898 PHE cc_start: 0.8129 (t80) cc_final: 0.7617 (t80) REVERT: A 983 GLU cc_start: 0.7768 (pp20) cc_final: 0.7431 (pm20) outliers start: 20 outliers final: 7 residues processed: 129 average time/residue: 0.5317 time to fit residues: 73.9373 Evaluate side-chains 127 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain B residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.0170 chunk 105 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.192589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158697 restraints weight = 12111.944| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.99 r_work: 0.3763 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1223 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= 0.144 Angle : 0.540 6.371 12737 Z= 0.264 Chirality : 0.040 0.147 1415 Planarity : 0.004 0.047 1665 Dihedral : 4.997 44.117 1259 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.31 % Allowed : 12.94 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.25), residues: 1147 helix: 1.16 (0.24), residues: 458 sheet: 0.18 (0.39), residues: 155 loop : -0.15 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 934 TYR 0.012 0.002 TYR A 996 PHE 0.012 0.001 PHE A 146 TRP 0.013 0.001 TRP A 903 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9374) covalent geometry : angle 0.53971 (12735) SS BOND : bond 0.00554 ( 1) SS BOND : angle 0.99137 ( 2) hydrogen bonds : bond 0.03373 ( 438) hydrogen bonds : angle 4.77634 ( 1209) Misc. bond : bond 0.00002 ( 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 142 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.308 Fit side-chains REVERT: A 54 MET cc_start: 0.6083 (ttm) cc_final: 0.5848 (ttm) REVERT: A 208 TRP cc_start: 0.6717 (m-10) cc_final: 0.6472 (m-10) REVERT: A 406 ASP cc_start: 0.6249 (t0) cc_final: 0.5974 (t0) REVERT: A 538 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6571 (mm) REVERT: A 580 ASN cc_start: 0.7404 (m-40) cc_final: 0.7163 (m110) REVERT: A 685 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6848 (mm-40) REVERT: A 721 MET cc_start: 0.4280 (mpp) cc_final: 0.3990 (mpp) REVERT: A 860 LEU cc_start: 0.8150 (tp) cc_final: 0.7914 (tp) REVERT: A 898 PHE cc_start: 0.8101 (t80) cc_final: 0.7649 (t80) REVERT: A 982 TYR cc_start: 0.8380 (m-80) cc_final: 0.8085 (m-80) REVERT: A 983 GLU cc_start: 0.7734 (pp20) cc_final: 0.7419 (pm20) outliers start: 13 outliers final: 6 residues processed: 137 average time/residue: 0.5401 time to fit residues: 79.7542 Evaluate side-chains 132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 88 optimal weight: 0.3980 chunk 109 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 53 optimal weight: 0.0980 chunk 14 optimal weight: 0.0670 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 931 GLN B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.194248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.160579 restraints weight = 12190.810| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.01 r_work: 0.3786 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9376 Z= 0.099 Angle : 0.507 6.800 12737 Z= 0.247 Chirality : 0.038 0.136 1415 Planarity : 0.004 0.043 1665 Dihedral : 4.695 43.389 1259 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.82 % Allowed : 13.04 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.25), residues: 1147 helix: 1.46 (0.24), residues: 457 sheet: 0.20 (0.39), residues: 155 loop : -0.08 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 287 TYR 0.011 0.001 TYR A 996 PHE 0.009 0.001 PHE A 146 TRP 0.016 0.001 TRP A 903 HIS 0.003 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9374) covalent geometry : angle 0.50724 (12735) SS BOND : bond 0.00443 ( 1) SS BOND : angle 0.73162 ( 2) hydrogen bonds : bond 0.02917 ( 438) hydrogen bonds : angle 4.55784 ( 1209) Misc. bond : bond 0.00006 ( 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 146 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.340 Fit side-chains REVERT: A 208 TRP cc_start: 0.6704 (m-10) cc_final: 0.6437 (m-10) REVERT: A 406 ASP cc_start: 0.6110 (t0) cc_final: 0.5848 (t0) REVERT: A 538 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6597 (mm) REVERT: A 580 ASN cc_start: 0.7386 (m-40) cc_final: 0.7131 (m110) REVERT: A 685 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6739 (mm-40) REVERT: A 721 MET cc_start: 0.4208 (mpp) cc_final: 0.3927 (mpp) REVERT: A 754 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6130 (mm) REVERT: A 860 LEU cc_start: 0.8136 (tp) cc_final: 0.7895 (tp) REVERT: A 898 PHE cc_start: 0.8071 (t80) cc_final: 0.7605 (t80) REVERT: A 982 TYR cc_start: 0.8378 (m-80) cc_final: 0.8061 (m-80) REVERT: A 983 GLU cc_start: 0.7768 (pp20) cc_final: 0.7467 (pm20) outliers start: 18 outliers final: 10 residues processed: 139 average time/residue: 0.5054 time to fit residues: 75.8119 Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 420 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 98 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 931 GLN B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.192632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158446 restraints weight = 12116.059| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.01 r_work: 0.3768 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9376 Z= 0.142 Angle : 0.550 9.767 12737 Z= 0.264 Chirality : 0.040 0.200 1415 Planarity : 0.004 0.043 1665 Dihedral : 4.746 42.178 1259 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.02 % Allowed : 13.14 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.25), residues: 1147 helix: 1.39 (0.24), residues: 458 sheet: 0.16 (0.40), residues: 155 loop : -0.11 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 287 TYR 0.012 0.002 TYR A 996 PHE 0.010 0.001 PHE A 146 TRP 0.017 0.001 TRP A 903 HIS 0.006 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9374) covalent geometry : angle 0.54989 (12735) SS BOND : bond 0.00519 ( 1) SS BOND : angle 0.92024 ( 2) hydrogen bonds : bond 0.03156 ( 438) hydrogen bonds : angle 4.60300 ( 1209) Misc. bond : bond 0.00006 ( 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 152 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 208 TRP cc_start: 0.6660 (m-10) cc_final: 0.6424 (m-10) REVERT: A 293 PHE cc_start: 0.7972 (m-80) cc_final: 0.7702 (m-80) REVERT: A 406 ASP cc_start: 0.6175 (t0) cc_final: 0.5908 (t0) REVERT: A 490 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7411 (mmmt) REVERT: A 538 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6644 (mm) REVERT: A 580 ASN cc_start: 0.7435 (m-40) cc_final: 0.7201 (m110) REVERT: A 685 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6762 (mm-40) REVERT: A 721 MET cc_start: 0.4173 (mpp) cc_final: 0.3917 (mpp) REVERT: A 754 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6136 (mm) REVERT: A 898 PHE cc_start: 0.8076 (t80) cc_final: 0.7638 (t80) REVERT: A 983 GLU cc_start: 0.7689 (pp20) cc_final: 0.7405 (pm20) outliers start: 20 outliers final: 15 residues processed: 144 average time/residue: 0.5493 time to fit residues: 85.2185 Evaluate side-chains 144 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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** 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 = 0.193210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.159053 restraints weight = 12202.506| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.02 r_work: 0.3777 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9376 Z= 0.122 Angle : 0.534 10.902 12737 Z= 0.256 Chirality : 0.039 0.145 1415 Planarity : 0.004 0.043 1665 Dihedral : 4.650 41.423 1259 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.22 % Allowed : 14.16 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.25), residues: 1147 helix: 1.48 (0.24), residues: 457 sheet: 0.19 (0.40), residues: 155 loop : -0.07 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 287 TYR 0.011 0.001 TYR A 996 PHE 0.012 0.001 PHE A 523 TRP 0.018 0.001 TRP A 903 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9374) covalent geometry : angle 0.53366 (12735) SS BOND : bond 0.00491 ( 1) SS BOND : angle 0.83555 ( 2) hydrogen bonds : bond 0.03013 ( 438) hydrogen bonds : angle 4.53429 ( 1209) Misc. bond : bond 0.00005 ( 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 151 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 208 TRP cc_start: 0.6687 (m-10) cc_final: 0.6461 (m-10) REVERT: A 406 ASP cc_start: 0.6138 (t0) cc_final: 0.5898 (t0) REVERT: A 538 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6468 (mt) REVERT: A 580 ASN cc_start: 0.7411 (m-40) cc_final: 0.7172 (m110) REVERT: A 685 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6751 (mm-40) REVERT: A 721 MET cc_start: 0.4147 (mpp) cc_final: 0.3871 (mpp) REVERT: A 754 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.6133 (mm) REVERT: A 860 LEU cc_start: 0.8131 (tp) cc_final: 0.7905 (tp) REVERT: A 898 PHE cc_start: 0.8065 (t80) cc_final: 0.7611 (t80) REVERT: A 983 GLU cc_start: 0.7695 (pp20) cc_final: 0.7414 (pm20) outliers start: 22 outliers final: 16 residues processed: 142 average time/residue: 0.5216 time to fit residues: 79.9822 Evaluate side-chains 144 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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** B 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.193006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.158249 restraints weight = 12057.677| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.06 r_work: 0.3761 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1723 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= 0.159 Angle : 0.562 11.460 12737 Z= 0.271 Chirality : 0.040 0.143 1415 Planarity : 0.004 0.044 1665 Dihedral : 4.762 40.023 1259 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.02 % Allowed : 14.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.25), residues: 1147 helix: 1.37 (0.24), residues: 458 sheet: 0.15 (0.39), residues: 155 loop : -0.15 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 287 TYR 0.013 0.002 TYR A 996 PHE 0.020 0.001 PHE A 293 TRP 0.022 0.002 TRP A 903 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9374) covalent geometry : angle 0.56155 (12735) SS BOND : bond 0.00554 ( 1) SS BOND : angle 0.99887 ( 2) hydrogen bonds : bond 0.03255 ( 438) hydrogen bonds : angle 4.60092 ( 1209) Misc. bond : bond 0.00011 ( 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 146 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.366 Fit side-chains REVERT: A 208 TRP cc_start: 0.6698 (m-10) cc_final: 0.6464 (m-10) REVERT: A 406 ASP cc_start: 0.6198 (t0) cc_final: 0.5927 (t0) REVERT: A 580 ASN cc_start: 0.7437 (m-40) cc_final: 0.7151 (m110) REVERT: A 685 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6759 (mm-40) REVERT: A 721 MET cc_start: 0.4108 (mpp) cc_final: 0.3840 (mpp) REVERT: A 754 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6148 (mm) REVERT: A 898 PHE cc_start: 0.8094 (t80) cc_final: 0.7630 (t80) REVERT: A 983 GLU cc_start: 0.7714 (pp20) cc_final: 0.7425 (pm20) outliers start: 20 outliers final: 14 residues processed: 140 average time/residue: 0.5028 time to fit residues: 75.9030 Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 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 A residue 754 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 23 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.193234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.159624 restraints weight = 12014.342| |-----------------------------------------------------------------------------| 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: 0.3609 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9376 Z= 0.145 Angle : 0.554 12.066 12737 Z= 0.267 Chirality : 0.040 0.141 1415 Planarity : 0.004 0.044 1665 Dihedral : 4.640 38.837 1257 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.02 % Allowed : 14.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.25), residues: 1147 helix: 1.39 (0.24), residues: 458 sheet: 0.15 (0.40), residues: 155 loop : -0.13 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 287 TYR 0.017 0.002 TYR A 434 PHE 0.013 0.001 PHE A 388 TRP 0.025 0.002 TRP A 903 HIS 0.006 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9374) covalent geometry : angle 0.55405 (12735) SS BOND : bond 0.00536 ( 1) SS BOND : angle 0.93122 ( 2) hydrogen bonds : bond 0.03162 ( 438) hydrogen bonds : angle 4.56471 ( 1209) Misc. bond : bond 0.00010 ( 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 143 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.346 Fit side-chains REVERT: A 208 TRP cc_start: 0.6726 (m-10) cc_final: 0.6491 (m-10) REVERT: A 406 ASP cc_start: 0.6140 (t0) cc_final: 0.5880 (t0) REVERT: A 489 ARG cc_start: 0.6626 (ttp-170) cc_final: 0.6414 (ttp-170) REVERT: A 580 ASN cc_start: 0.7434 (m-40) cc_final: 0.7168 (m110) REVERT: A 685 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6782 (mm-40) REVERT: A 721 MET cc_start: 0.4207 (mpp) cc_final: 0.3914 (mpp) REVERT: A 754 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6176 (mm) REVERT: A 898 PHE cc_start: 0.8089 (t80) cc_final: 0.7664 (t80) REVERT: A 983 GLU cc_start: 0.7752 (pp20) cc_final: 0.7472 (pm20) outliers start: 20 outliers final: 15 residues processed: 136 average time/residue: 0.5500 time to fit residues: 80.3727 Evaluate side-chains 138 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 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 A residue 754 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 66 optimal weight: 0.1980 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 29 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 112 optimal weight: 0.0170 overall best weight: 0.2218 ------------------------------------------------------------------------------- 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** B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.194996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161775 restraints weight = 12084.998| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.01 r_work: 0.3795 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1868 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= 0.105 Angle : 0.540 12.357 12737 Z= 0.258 Chirality : 0.039 0.140 1415 Planarity : 0.004 0.044 1665 Dihedral : 4.439 38.326 1257 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.92 % Allowed : 15.07 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.25), residues: 1147 helix: 1.56 (0.24), residues: 458 sheet: 0.22 (0.40), residues: 155 loop : -0.04 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 287 TYR 0.012 0.001 TYR A 434 PHE 0.012 0.001 PHE A 388 TRP 0.027 0.001 TRP A 903 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9374) covalent geometry : angle 0.54030 (12735) SS BOND : bond 0.00433 ( 1) SS BOND : angle 0.63398 ( 2) hydrogen bonds : bond 0.02884 ( 438) hydrogen bonds : angle 4.44387 ( 1209) Misc. bond : bond 0.00002 ( 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 138 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.355 Fit side-chains REVERT: A 208 TRP cc_start: 0.6716 (m-10) cc_final: 0.6490 (m-10) REVERT: A 391 LEU cc_start: 0.7244 (mt) cc_final: 0.6518 (mp) REVERT: A 406 ASP cc_start: 0.6051 (t0) cc_final: 0.5808 (t0) REVERT: A 489 ARG cc_start: 0.6601 (ttp-170) cc_final: 0.6394 (ttp-170) REVERT: A 580 ASN cc_start: 0.7432 (m-40) cc_final: 0.7140 (m110) REVERT: A 582 LYS cc_start: 0.7277 (mptm) cc_final: 0.7039 (mptm) REVERT: A 685 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6819 (mm-40) REVERT: A 721 MET cc_start: 0.4177 (mpp) cc_final: 0.3867 (mpp) REVERT: A 754 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6184 (mm) REVERT: A 898 PHE cc_start: 0.8076 (t80) cc_final: 0.7635 (t80) outliers start: 19 outliers final: 16 residues processed: 131 average time/residue: 0.5240 time to fit residues: 74.2094 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 : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 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 21 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 ASN ** 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 = 0.4300 r_free = 0.4300 target = 0.192245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158457 restraints weight = 12003.566| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.97 r_work: 0.3767 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1951 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= 0.191 Angle : 0.605 13.277 12737 Z= 0.292 Chirality : 0.041 0.143 1415 Planarity : 0.004 0.043 1665 Dihedral : 4.690 36.292 1257 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.82 % Allowed : 15.47 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1147 helix: 1.29 (0.24), residues: 459 sheet: 0.11 (0.40), residues: 155 loop : -0.18 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 287 TYR 0.014 0.002 TYR A 982 PHE 0.010 0.001 PHE A 146 TRP 0.024 0.002 TRP A 903 HIS 0.007 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9374) covalent geometry : angle 0.60445 (12735) SS BOND : bond 0.00552 ( 1) SS BOND : angle 1.08503 ( 2) hydrogen bonds : bond 0.03397 ( 438) hydrogen bonds : angle 4.62506 ( 1209) Misc. bond : bond 0.00014 ( 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 138 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.358 Fit side-chains REVERT: A 208 TRP cc_start: 0.6761 (m-10) cc_final: 0.6509 (m-10) REVERT: A 391 LEU cc_start: 0.7369 (mt) cc_final: 0.6621 (mp) REVERT: A 406 ASP cc_start: 0.6175 (t0) cc_final: 0.5897 (t0) REVERT: A 580 ASN cc_start: 0.7495 (m-40) cc_final: 0.7190 (m110) REVERT: A 582 LYS cc_start: 0.7281 (mptm) cc_final: 0.7049 (mptm) REVERT: A 685 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6777 (mm-40) REVERT: A 721 MET cc_start: 0.4107 (mpp) cc_final: 0.3832 (mpp) REVERT: A 754 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6248 (mm) REVERT: A 898 PHE cc_start: 0.8093 (t80) cc_final: 0.7743 (t80) REVERT: A 983 GLU cc_start: 0.7551 (pp20) cc_final: 0.7227 (pm20) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.5459 time to fit residues: 78.2090 Evaluate side-chains 134 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 88 optimal weight: 0.4980 chunk 112 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 0.0040 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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** B 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.193033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159277 restraints weight = 12008.773| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.98 r_work: 0.3776 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: 0.7045 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9376 Z= 0.152 Angle : 0.587 13.441 12737 Z= 0.283 Chirality : 0.040 0.142 1415 Planarity : 0.004 0.055 1665 Dihedral : 4.661 36.974 1257 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.62 % Allowed : 15.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.25), residues: 1147 helix: 1.31 (0.24), residues: 458 sheet: 0.10 (0.40), residues: 155 loop : -0.17 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 934 TYR 0.013 0.002 TYR A 434 PHE 0.010 0.001 PHE A 146 TRP 0.024 0.002 TRP A 903 HIS 0.007 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9374) covalent geometry : angle 0.58695 (12735) SS BOND : bond 0.00539 ( 1) SS BOND : angle 0.94910 ( 2) hydrogen bonds : bond 0.03239 ( 438) hydrogen bonds : angle 4.57086 ( 1209) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3951.15 seconds wall clock time: 68 minutes 3.59 seconds (4083.59 seconds total)