Starting phenix.real_space_refine on Thu Jul 2 12:26:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywi_39634/07_2026/8ywi_39634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywi_39634/07_2026/8ywi_39634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ywi_39634/07_2026/8ywi_39634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywi_39634/07_2026/8ywi_39634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ywi_39634/07_2026/8ywi_39634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywi_39634/07_2026/8ywi_39634.map" } resolution = 2.7 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= 0.028 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: 6 Type Number sf(0) Gaussians P 37 5.49 5 Mg 1 5.21 5 S 51 5.16 5 C 5463 2.51 5 N 1477 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8710 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7983 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 934} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 287 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.43, per 1000 atoms: 0.16 Number of scatterers: 8710 At special positions: 0 Unit cell: (94.53, 106.26, 101.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 37 15.00 Mg 1 11.99 O 1681 8.00 N 1477 7.00 C 5463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 258.1 milliseconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1872 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 49.4% alpha, 16.8% beta 14 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.793A pdb=" N GLU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.799A pdb=" N GLU A 117 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 removed outlier: 3.800A pdb=" N ARG A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.742A pdb=" N PHE A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.739A pdb=" N CYS A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 410 through 436 removed outlier: 3.799A pdb=" N CYS A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 4.101A pdb=" N ASP A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.626A pdb=" N HIS A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 580 through 609 removed outlier: 3.723A pdb=" N LYS A 584 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 646 removed outlier: 3.835A pdb=" N PHE A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 642 " --> pdb=" O MET A 638 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 646 " --> pdb=" O TYR A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 678 removed outlier: 3.717A pdb=" N ALA A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 709 Processing helix chain 'A' and resid 713 through 748 removed outlier: 3.701A pdb=" N THR A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 814 removed outlier: 3.601A pdb=" N LYS A 804 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 813 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 814 " --> pdb=" O ILE A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 840 removed outlier: 3.788A pdb=" N ILE A 830 " --> pdb=" O PRO A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.977A pdb=" N GLN A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP A 845 " --> pdb=" O MET A 842 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 841 through 845' Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.687A pdb=" N SER A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS A 882 " --> pdb=" O GLN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.523A pdb=" N PHE A 889 " --> pdb=" O ALA A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 939 through 956 removed outlier: 3.971A pdb=" N TYR A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLY A 950 " --> pdb=" O ASN A 946 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 951 " --> pdb=" O TYR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 963 removed outlier: 3.704A pdb=" N PHE A 962 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 991 removed outlier: 3.606A pdb=" N TYR A 974 " --> pdb=" O ASN A 970 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.256A pdb=" N SER A 54 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS A 184 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 62 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 74 removed outlier: 7.848A pdb=" N ALA A 481 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG A 106 " --> pdb=" O ALA A 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268 removed outlier: 4.144A pdb=" N ALA A 249 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 293 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 346 removed outlier: 5.507A pdb=" N LYS A 339 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 355 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 345 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 508 removed outlier: 5.324A pdb=" N TYR A 756 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP A 517 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 758 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 515 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY A 686 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR A 692 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508 removed outlier: 4.854A pdb=" N ILE A 774 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 763 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR A 772 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 765 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LYS A 770 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA8, first strand: chain 'A' and resid 852 through 855 411 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2281 1.33 - 1.45: 1784 1.45 - 1.57: 4770 1.57 - 1.69: 71 1.69 - 1.81: 81 Bond restraints: 8987 Sorted by residual: bond pdb=" O3B TTP T1101 " pdb=" PG TTP T1101 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" O3A TTP T1101 " pdb=" PB TTP T1101 " ideal model delta sigma weight residual 1.675 1.599 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3' DA T 7 " pdb=" C2' DA T 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.76e+00 bond pdb=" C3' DT P 23 " pdb=" C2' DT P 23 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.96e+00 bond pdb=" C3' DT P 22 " pdb=" C2' DT P 22 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.43e+00 ... (remaining 8982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 12068 2.12 - 4.25: 203 4.25 - 6.37: 24 6.37 - 8.49: 4 8.49 - 10.61: 2 Bond angle restraints: 12301 Sorted by residual: angle pdb=" C LEU A 193 " pdb=" N VAL A 194 " pdb=" CA VAL A 194 " ideal model delta sigma weight residual 121.97 132.58 -10.61 1.80e+00 3.09e-01 3.48e+01 angle pdb=" C ASP A 230 " pdb=" N VAL A 231 " pdb=" CA VAL A 231 " ideal model delta sigma weight residual 121.97 131.44 -9.47 1.80e+00 3.09e-01 2.77e+01 angle pdb=" N3 DT P 15 " pdb=" C4 DT P 15 " pdb=" O4 DT P 15 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT T 8 " pdb=" C4 DT T 8 " pdb=" O4 DT T 8 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT P 23 " pdb=" C4 DT P 23 " pdb=" O4 DT P 23 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 12296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 4937 25.94 - 51.87: 386 51.87 - 77.81: 45 77.81 - 103.74: 2 103.74 - 129.68: 1 Dihedral angle restraints: 5371 sinusoidal: 2464 harmonic: 2907 Sorted by residual: dihedral pdb=" O5' TTP T1101 " pdb=" O3A TTP T1101 " pdb=" PA TTP T1101 " pdb=" PB TTP T1101 " ideal model delta sinusoidal sigma weight residual 184.45 54.77 129.68 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CA PHE A 240 " pdb=" C PHE A 240 " pdb=" N TRP A 241 " pdb=" CA TRP A 241 " ideal model delta harmonic sigma weight residual 180.00 163.35 16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASP A 837 " pdb=" CB ASP A 837 " pdb=" CG ASP A 837 " pdb=" OD1 ASP A 837 " ideal model delta sinusoidal sigma weight residual -30.00 -86.24 56.24 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 5368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1276 0.096 - 0.192: 54 0.192 - 0.288: 0 0.288 - 0.384: 1 0.384 - 0.480: 1 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CB VAL A 231 " pdb=" CA VAL A 231 " pdb=" CG1 VAL A 231 " pdb=" CG2 VAL A 231 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CB VAL A 194 " pdb=" CA VAL A 194 " pdb=" CG1 VAL A 194 " pdb=" CG2 VAL A 194 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE A 792 " pdb=" CA ILE A 792 " pdb=" CG1 ILE A 792 " pdb=" CG2 ILE A 792 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 1329 not shown) Planarity restraints: 1449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 287 " 0.062 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO A 288 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 164 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 165 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 824 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO A 825 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 825 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 825 " 0.033 5.00e-02 4.00e+02 ... (remaining 1446 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 842 2.75 - 3.29: 7895 3.29 - 3.82: 13752 3.82 - 4.36: 15611 4.36 - 4.90: 27490 Nonbonded interactions: 65590 Sorted by model distance: nonbonded pdb=" OD2 ASP A 517 " pdb="MG MG A1301 " model vdw 2.209 2.170 nonbonded pdb=" OD2 ASP A 689 " pdb=" O1A TTP T1101 " model vdw 2.212 3.040 nonbonded pdb=" OE2 GLU A 644 " pdb=" OG SER A 650 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR A 146 " pdb=" OD2 ASP A 149 " model vdw 2.259 3.040 nonbonded pdb=" O PHE A 518 " pdb="MG MG A1301 " model vdw 2.305 2.170 ... (remaining 65585 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: 2.980 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 8.750 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.004 0.139 8987 Z= 0.274 Angle : 0.643 10.613 12301 Z= 0.414 Chirality : 0.044 0.480 1332 Planarity : 0.005 0.094 1449 Dihedral : 16.856 129.680 3499 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.82 % Allowed : 4.82 % Favored : 94.36 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.28), residues: 976 helix: 2.23 (0.25), residues: 443 sheet: 0.30 (0.40), residues: 173 loop : -1.33 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 744 TYR 0.010 0.001 TYR A 756 PHE 0.019 0.001 PHE A 324 TRP 0.014 0.001 TRP A 325 HIS 0.004 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.27 ( 8987) covalent geometry : angle 0.64265 / 0.41 (12301) hydrogen bonds : bond 0.13802 / 9.60 ( 440) hydrogen bonds : angle 4.77211 / 3.31 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 599 GLU cc_start: 0.7457 (tp30) cc_final: 0.7104 (tp30) REVERT: A 601 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7938 (ttpt) REVERT: A 744 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7666 (ttm110) REVERT: A 882 HIS cc_start: 0.6987 (t70) cc_final: 0.6766 (t70) outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.5341 time to fit residues: 111.6946 Evaluate side-chains 180 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 29 ASN A 145 ASN A 778 ASN A 841 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109261 restraints weight = 12388.146| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.66 r_work: 0.3425 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8987 Z= 0.168 Angle : 0.602 10.832 12301 Z= 0.328 Chirality : 0.044 0.451 1332 Planarity : 0.005 0.062 1449 Dihedral : 16.688 114.133 1508 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.43 % Favored : 93.95 % Rotamer: Outliers : 1.93 % Allowed : 10.81 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.28), residues: 976 helix: 2.28 (0.25), residues: 447 sheet: 0.27 (0.40), residues: 173 loop : -1.30 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 744 TYR 0.025 0.001 TYR A 756 PHE 0.015 0.002 PHE A 85 TRP 0.015 0.001 TRP A 325 HIS 0.003 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 8987) covalent geometry : angle 0.60206 / 0.33 (12301) hydrogen bonds : bond 0.05711 / 3.83 ( 440) hydrogen bonds : angle 4.05031 / 2.79 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8196 (tt) REVERT: A 191 GLU cc_start: 0.7819 (pm20) cc_final: 0.7481 (pm20) REVERT: A 248 LEU cc_start: 0.8528 (mt) cc_final: 0.8303 (mp) REVERT: A 402 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.7026 (ttp) REVERT: A 598 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: A 599 GLU cc_start: 0.8107 (tp30) cc_final: 0.7714 (tp30) REVERT: A 644 GLU cc_start: 0.7916 (tp30) cc_final: 0.7654 (mm-30) REVERT: A 728 SER cc_start: 0.8972 (m) cc_final: 0.8678 (m) REVERT: A 744 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7794 (ttm110) REVERT: A 841 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7364 (t0) REVERT: A 882 HIS cc_start: 0.7884 (t70) cc_final: 0.7521 (t70) REVERT: A 893 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 930 GLU cc_start: 0.8147 (tp30) cc_final: 0.7872 (tm-30) REVERT: A 974 TYR cc_start: 0.8024 (t80) cc_final: 0.7490 (t80) REVERT: A 978 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7934 (tpp-160) REVERT: A 988 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8054 (mt0) outliers start: 17 outliers final: 10 residues processed: 189 average time/residue: 0.5476 time to fit residues: 109.3982 Evaluate side-chains 190 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 988 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 530 ASN A 778 ASN A 841 ASN A 873 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.123944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108608 restraints weight = 12359.392| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.66 r_work: 0.3417 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8987 Z= 0.167 Angle : 0.580 10.324 12301 Z= 0.318 Chirality : 0.043 0.492 1332 Planarity : 0.004 0.048 1449 Dihedral : 16.577 108.997 1506 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.23 % Favored : 94.16 % Rotamer: Outliers : 2.96 % Allowed : 12.29 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.28), residues: 976 helix: 2.28 (0.25), residues: 447 sheet: 0.22 (0.39), residues: 173 loop : -1.29 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.021 0.001 TYR A 756 PHE 0.016 0.001 PHE A 85 TRP 0.011 0.001 TRP A 325 HIS 0.010 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 8987) covalent geometry : angle 0.58041 / 0.32 (12301) hydrogen bonds : bond 0.05546 / 3.73 ( 440) hydrogen bonds : angle 3.97024 / 2.73 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8128 (tt) REVERT: A 248 LEU cc_start: 0.8523 (mt) cc_final: 0.8297 (mp) REVERT: A 598 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: A 599 GLU cc_start: 0.8145 (tp30) cc_final: 0.7744 (tp30) REVERT: A 728 SER cc_start: 0.8977 (m) cc_final: 0.8713 (m) REVERT: A 744 ARG cc_start: 0.8441 (ttp80) cc_final: 0.7848 (ttm170) REVERT: A 882 HIS cc_start: 0.7872 (t70) cc_final: 0.7514 (t70) REVERT: A 974 TYR cc_start: 0.8100 (t80) cc_final: 0.7763 (t80) REVERT: A 988 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8057 (mt0) outliers start: 26 outliers final: 11 residues processed: 189 average time/residue: 0.5641 time to fit residues: 113.0099 Evaluate side-chains 189 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 988 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.8980 chunk 23 optimal weight: 0.0010 chunk 37 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.124862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109496 restraints weight = 12485.968| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.67 r_work: 0.3429 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8987 Z= 0.136 Angle : 0.560 9.984 12301 Z= 0.307 Chirality : 0.042 0.520 1332 Planarity : 0.004 0.044 1449 Dihedral : 16.431 106.555 1506 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.23 % Favored : 94.16 % Rotamer: Outliers : 2.28 % Allowed : 14.90 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.28), residues: 976 helix: 2.38 (0.25), residues: 449 sheet: 0.16 (0.39), residues: 173 loop : -1.25 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 977 TYR 0.020 0.001 TYR A 756 PHE 0.017 0.001 PHE A 85 TRP 0.010 0.001 TRP A 241 HIS 0.007 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 8987) covalent geometry : angle 0.56018 / 0.31 (12301) hydrogen bonds : bond 0.04891 / 3.29 ( 440) hydrogen bonds : angle 3.85705 / 2.66 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8124 (tt) REVERT: A 336 TYR cc_start: 0.8673 (m-80) cc_final: 0.8426 (m-80) REVERT: A 598 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: A 599 GLU cc_start: 0.8132 (tp30) cc_final: 0.7742 (tp30) REVERT: A 644 GLU cc_start: 0.7890 (tp30) cc_final: 0.7648 (mm-30) REVERT: A 728 SER cc_start: 0.8972 (m) cc_final: 0.8718 (m) REVERT: A 744 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7833 (ttm110) REVERT: A 882 HIS cc_start: 0.7822 (t70) cc_final: 0.7471 (t70) outliers start: 20 outliers final: 10 residues processed: 181 average time/residue: 0.5823 time to fit residues: 111.7869 Evaluate side-chains 185 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 598 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108687 restraints weight = 12411.349| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.67 r_work: 0.3416 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8987 Z= 0.156 Angle : 0.564 9.932 12301 Z= 0.309 Chirality : 0.044 0.567 1332 Planarity : 0.004 0.042 1449 Dihedral : 16.398 105.776 1506 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.12 % Favored : 94.26 % Rotamer: Outliers : 2.50 % Allowed : 16.04 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.28), residues: 976 helix: 2.35 (0.25), residues: 447 sheet: 0.14 (0.39), residues: 173 loop : -1.26 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 977 TYR 0.021 0.001 TYR A 756 PHE 0.016 0.001 PHE A 85 TRP 0.010 0.001 TRP A 241 HIS 0.008 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 8987) covalent geometry : angle 0.56414 / 0.31 (12301) hydrogen bonds : bond 0.05115 / 3.46 ( 440) hydrogen bonds : angle 3.84823 / 2.65 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.312 Fit side-chains REVERT: A 182 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 248 LEU cc_start: 0.8562 (mp) cc_final: 0.8309 (mt) REVERT: A 598 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: A 599 GLU cc_start: 0.8144 (tp30) cc_final: 0.7759 (tp30) REVERT: A 728 SER cc_start: 0.8968 (m) cc_final: 0.8708 (m) REVERT: A 744 ARG cc_start: 0.8443 (ttp80) cc_final: 0.7822 (ttm170) REVERT: A 841 ASN cc_start: 0.7681 (t0) cc_final: 0.7267 (t0) REVERT: A 882 HIS cc_start: 0.7839 (t70) cc_final: 0.7477 (t70) outliers start: 22 outliers final: 13 residues processed: 187 average time/residue: 0.5100 time to fit residues: 101.2405 Evaluate side-chains 193 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 688 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108696 restraints weight = 12383.077| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.67 r_work: 0.3416 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8987 Z= 0.153 Angle : 0.580 9.647 12301 Z= 0.313 Chirality : 0.044 0.621 1332 Planarity : 0.004 0.041 1449 Dihedral : 16.392 105.549 1506 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.33 % Favored : 94.06 % Rotamer: Outliers : 2.28 % Allowed : 16.50 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.28), residues: 976 helix: 2.38 (0.25), residues: 449 sheet: 0.08 (0.38), residues: 178 loop : -1.26 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 977 TYR 0.021 0.001 TYR A 555 PHE 0.020 0.001 PHE A 889 TRP 0.010 0.001 TRP A 241 HIS 0.008 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8987) covalent geometry : angle 0.58009 / 0.31 (12301) hydrogen bonds : bond 0.05041 / 3.40 ( 440) hydrogen bonds : angle 3.84649 / 2.65 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.246 Fit side-chains REVERT: A 182 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8132 (tt) REVERT: A 185 ARG cc_start: 0.7734 (mmt90) cc_final: 0.7282 (mtt90) REVERT: A 248 LEU cc_start: 0.8581 (mp) cc_final: 0.8320 (mt) REVERT: A 598 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: A 599 GLU cc_start: 0.8142 (tp30) cc_final: 0.7764 (tp30) REVERT: A 644 GLU cc_start: 0.7953 (tp30) cc_final: 0.7714 (mm-30) REVERT: A 728 SER cc_start: 0.8968 (m) cc_final: 0.8711 (m) REVERT: A 744 ARG cc_start: 0.8455 (ttp80) cc_final: 0.7837 (ttm170) REVERT: A 841 ASN cc_start: 0.7715 (t0) cc_final: 0.7275 (t0) REVERT: A 882 HIS cc_start: 0.7828 (t70) cc_final: 0.7466 (t70) outliers start: 20 outliers final: 12 residues processed: 189 average time/residue: 0.5434 time to fit residues: 108.7173 Evaluate side-chains 192 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 988 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 227 GLN A 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.123562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.108234 restraints weight = 12476.739| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.67 r_work: 0.3409 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8987 Z= 0.164 Angle : 0.587 9.673 12301 Z= 0.317 Chirality : 0.045 0.656 1332 Planarity : 0.004 0.041 1449 Dihedral : 16.404 106.000 1506 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.23 % Favored : 94.16 % Rotamer: Outliers : 2.39 % Allowed : 16.84 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.27), residues: 976 helix: 2.32 (0.25), residues: 447 sheet: -0.01 (0.38), residues: 180 loop : -1.25 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 977 TYR 0.019 0.001 TYR A 555 PHE 0.014 0.002 PHE A 889 TRP 0.009 0.001 TRP A 241 HIS 0.010 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 8987) covalent geometry : angle 0.58727 / 0.32 (12301) hydrogen bonds : bond 0.05197 / 3.51 ( 440) hydrogen bonds : angle 3.87625 / 2.67 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.316 Fit side-chains REVERT: A 182 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8133 (tt) REVERT: A 248 LEU cc_start: 0.8612 (mp) cc_final: 0.8351 (mt) REVERT: A 598 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: A 599 GLU cc_start: 0.8158 (tp30) cc_final: 0.7794 (tp30) REVERT: A 728 SER cc_start: 0.8964 (m) cc_final: 0.8719 (m) REVERT: A 744 ARG cc_start: 0.8458 (ttp80) cc_final: 0.7869 (ttm170) REVERT: A 841 ASN cc_start: 0.7756 (t0) cc_final: 0.7359 (t0) REVERT: A 882 HIS cc_start: 0.7823 (t70) cc_final: 0.7471 (t70) outliers start: 21 outliers final: 13 residues processed: 195 average time/residue: 0.5316 time to fit residues: 109.9237 Evaluate side-chains 198 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 932 LYS Chi-restraints excluded: chain A residue 988 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 65 optimal weight: 0.0070 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 227 GLN A 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.125307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109974 restraints weight = 12323.238| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.67 r_work: 0.3435 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8987 Z= 0.125 Angle : 0.567 10.307 12301 Z= 0.306 Chirality : 0.043 0.669 1332 Planarity : 0.004 0.039 1449 Dihedral : 16.310 105.128 1506 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.92 % Favored : 94.47 % Rotamer: Outliers : 2.50 % Allowed : 17.29 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.28), residues: 976 helix: 2.44 (0.25), residues: 449 sheet: 0.00 (0.38), residues: 180 loop : -1.25 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.020 0.001 TYR A 974 PHE 0.013 0.001 PHE A 889 TRP 0.011 0.001 TRP A 241 HIS 0.007 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 8987) covalent geometry : angle 0.56690 / 0.31 (12301) hydrogen bonds : bond 0.04388 / 2.95 ( 440) hydrogen bonds : angle 3.76580 / 2.60 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.298 Fit side-chains REVERT: A 182 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 598 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8017 (mt0) REVERT: A 599 GLU cc_start: 0.8153 (tp30) cc_final: 0.7789 (tp30) REVERT: A 728 SER cc_start: 0.8950 (m) cc_final: 0.8715 (m) REVERT: A 744 ARG cc_start: 0.8453 (ttp80) cc_final: 0.7863 (ttm110) REVERT: A 841 ASN cc_start: 0.7744 (t0) cc_final: 0.7389 (t0) REVERT: A 882 HIS cc_start: 0.7802 (t70) cc_final: 0.7452 (t70) REVERT: A 973 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6784 (tm-30) outliers start: 22 outliers final: 12 residues processed: 191 average time/residue: 0.5590 time to fit residues: 113.0695 Evaluate side-chains 196 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 988 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 227 GLN A 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.123487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108263 restraints weight = 12348.162| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.68 r_work: 0.3415 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8987 Z= 0.164 Angle : 0.590 9.901 12301 Z= 0.318 Chirality : 0.045 0.664 1332 Planarity : 0.004 0.045 1449 Dihedral : 16.342 105.889 1506 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.12 % Favored : 94.26 % Rotamer: Outliers : 2.28 % Allowed : 17.86 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.27), residues: 976 helix: 2.38 (0.25), residues: 445 sheet: -0.09 (0.38), residues: 180 loop : -1.27 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 977 TYR 0.018 0.001 TYR A 756 PHE 0.019 0.002 PHE A 889 TRP 0.008 0.001 TRP A 241 HIS 0.008 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8987) covalent geometry : angle 0.59037 / 0.32 (12301) hydrogen bonds : bond 0.05124 / 3.44 ( 440) hydrogen bonds : angle 3.85237 / 2.66 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.336 Fit side-chains REVERT: A 182 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8218 (tt) REVERT: A 248 LEU cc_start: 0.8606 (mp) cc_final: 0.8361 (mt) REVERT: A 598 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: A 599 GLU cc_start: 0.8144 (tp30) cc_final: 0.7770 (tp30) REVERT: A 644 GLU cc_start: 0.7891 (tp30) cc_final: 0.7686 (mm-30) REVERT: A 728 SER cc_start: 0.8960 (m) cc_final: 0.8701 (m) REVERT: A 744 ARG cc_start: 0.8427 (ttp80) cc_final: 0.7837 (ttm170) REVERT: A 841 ASN cc_start: 0.7794 (t0) cc_final: 0.7458 (t0) REVERT: A 873 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7815 (t70) REVERT: A 882 HIS cc_start: 0.7801 (t70) cc_final: 0.7441 (t70) outliers start: 20 outliers final: 11 residues processed: 190 average time/residue: 0.5544 time to fit residues: 111.5682 Evaluate side-chains 194 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 873 HIS Chi-restraints excluded: chain A residue 988 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 227 GLN A 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107895 restraints weight = 12332.015| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.67 r_work: 0.3412 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8987 Z= 0.169 Angle : 0.601 9.535 12301 Z= 0.322 Chirality : 0.045 0.646 1332 Planarity : 0.004 0.043 1449 Dihedral : 16.393 105.397 1506 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.33 % Favored : 94.06 % Rotamer: Outliers : 1.59 % Allowed : 18.43 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 976 helix: 2.36 (0.25), residues: 445 sheet: -0.11 (0.38), residues: 180 loop : -1.27 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.017 0.001 TYR A 555 PHE 0.016 0.002 PHE A 889 TRP 0.009 0.001 TRP A 568 HIS 0.008 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 8987) covalent geometry : angle 0.60070 / 0.32 (12301) hydrogen bonds : bond 0.05176 / 3.48 ( 440) hydrogen bonds : angle 3.87969 / 2.68 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.319 Fit side-chains REVERT: A 182 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8208 (tt) REVERT: A 248 LEU cc_start: 0.8603 (mp) cc_final: 0.8363 (mt) REVERT: A 598 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: A 599 GLU cc_start: 0.8157 (tp30) cc_final: 0.7780 (tp30) REVERT: A 644 GLU cc_start: 0.7889 (tp30) cc_final: 0.7684 (mm-30) REVERT: A 728 SER cc_start: 0.8970 (m) cc_final: 0.8710 (m) REVERT: A 744 ARG cc_start: 0.8432 (ttp80) cc_final: 0.7832 (ttm170) REVERT: A 841 ASN cc_start: 0.7813 (t0) cc_final: 0.7501 (t0) REVERT: A 882 HIS cc_start: 0.7816 (t70) cc_final: 0.7454 (t70) outliers start: 14 outliers final: 9 residues processed: 188 average time/residue: 0.5605 time to fit residues: 111.6292 Evaluate side-chains 191 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 632 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 227 GLN A 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.123441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.108172 restraints weight = 12354.061| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.68 r_work: 0.3416 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8987 Z= 0.155 Angle : 0.593 9.223 12301 Z= 0.318 Chirality : 0.044 0.552 1332 Planarity : 0.004 0.042 1449 Dihedral : 16.397 105.205 1506 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.12 % Favored : 94.26 % Rotamer: Outliers : 1.48 % Allowed : 18.89 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 976 helix: 2.37 (0.25), residues: 445 sheet: -0.11 (0.38), residues: 180 loop : -1.26 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.018 0.001 TYR A 756 PHE 0.020 0.001 PHE A 85 TRP 0.009 0.001 TRP A 241 HIS 0.008 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 8987) covalent geometry : angle 0.59271 / 0.32 (12301) hydrogen bonds : bond 0.05053 / 3.40 ( 440) hydrogen bonds : angle 3.88685 / 2.67 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.69 seconds wall clock time: 57 minutes 43.58 seconds (3463.58 seconds total)