Starting phenix.real_space_refine on Wed Aug 5 05:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywi_39634/08_2026/8ywi_39634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywi_39634/08_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_39634/08_2026/8ywi_39634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywi_39634/08_2026/8ywi_39634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ywi_39634/08_2026/8ywi_39634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywi_39634/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.95, per 1000 atoms: 0.22 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 189.6 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: 0.99 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: 1.74 Time building geometry restraints manager: 0.99 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: 3.450 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.950 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- 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= 0.275 Angle : 0.644 10.613 12301 Z= 0.416 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 0.64363 / 0.42 (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 : 0.295 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: 0.5929 time to fit residues: 123.8954 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 : 0.275 ------------------------------------------------------------------------------- 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: 3.9990 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 = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109266 restraints weight = 12404.292| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.66 r_work: 0.3425 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8987 Z= 0.168 Angle : 0.604 10.788 12301 Z= 0.330 Chirality : 0.044 0.460 1332 Planarity : 0.005 0.062 1449 Dihedral : 16.700 114.805 1508 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.43 % Favored : 93.95 % Rotamer: Outliers : 2.16 % Allowed : 10.47 % Favored : 87.37 % 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: 1.01 (0.28), residues: 976 helix: 2.30 (0.25), residues: 447 sheet: 0.27 (0.40), residues: 173 loop : -1.31 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 744 TYR 0.024 0.001 TYR A 756 PHE 0.015 0.002 PHE A 324 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 0.00369 / 0.17 ( 8987) covalent geometry : angle 0.60351 / 0.33 (12301) hydrogen bonds : bond 0.05750 / 3.86 ( 440) hydrogen bonds : angle 4.05815 / 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 200 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 191 GLU cc_start: 0.7824 (pm20) cc_final: 0.7475 (pm20) REVERT: A 248 LEU cc_start: 0.8514 (mt) cc_final: 0.8293 (mp) REVERT: A 402 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6988 (ttp) REVERT: A 598 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: A 599 GLU cc_start: 0.8125 (tp30) cc_final: 0.7725 (tp30) REVERT: A 644 GLU cc_start: 0.7907 (tp30) cc_final: 0.7624 (mm-30) REVERT: A 728 SER cc_start: 0.8973 (m) cc_final: 0.8677 (m) REVERT: A 744 ARG cc_start: 0.8431 (ttp80) cc_final: 0.7800 (ttm110) REVERT: A 841 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7370 (t0) REVERT: A 882 HIS cc_start: 0.7877 (t70) cc_final: 0.7514 (t70) REVERT: A 893 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7716 (mt-10) REVERT: A 930 GLU cc_start: 0.8145 (tp30) cc_final: 0.7882 (tm-30) REVERT: A 974 TYR cc_start: 0.8021 (t80) cc_final: 0.7562 (t80) REVERT: A 988 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8064 (mt0) outliers start: 19 outliers final: 11 residues processed: 188 average time/residue: 0.5741 time to fit residues: 114.2351 Evaluate side-chains 192 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 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 = 0.3723 r_free = 0.3723 target = 0.123924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108499 restraints weight = 12360.056| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.67 r_work: 0.3415 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8987 Z= 0.168 Angle : 0.583 10.319 12301 Z= 0.319 Chirality : 0.043 0.493 1332 Planarity : 0.004 0.048 1449 Dihedral : 16.561 108.802 1506 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.02 % Favored : 94.36 % Rotamer: Outliers : 2.84 % Allowed : 12.74 % Favored : 84.41 % 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: 2.26 (0.25), residues: 447 sheet: 0.23 (0.39), residues: 173 loop : -1.28 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 978 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 0.00373 / 0.17 ( 8987) covalent geometry : angle 0.58319 / 0.32 (12301) hydrogen bonds : bond 0.05554 / 3.73 ( 440) hydrogen bonds : angle 3.96796 / 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: 25 poor density : 179 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8128 (tt) REVERT: A 598 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: A 599 GLU cc_start: 0.8137 (tp30) cc_final: 0.7728 (tp30) REVERT: A 728 SER cc_start: 0.8969 (m) cc_final: 0.8701 (m) REVERT: A 744 ARG cc_start: 0.8420 (ttp80) cc_final: 0.7802 (ttm170) REVERT: A 882 HIS cc_start: 0.7872 (t70) cc_final: 0.7506 (t70) REVERT: A 893 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 988 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8068 (mt0) outliers start: 25 outliers final: 11 residues processed: 189 average time/residue: 0.5342 time to fit residues: 107.0521 Evaluate side-chains 191 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 0.0570 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 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: 0.7980 chunk 99 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.124163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.108862 restraints weight = 12494.214| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.65 r_work: 0.3421 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8987 Z= 0.148 Angle : 0.569 9.839 12301 Z= 0.311 Chirality : 0.043 0.532 1332 Planarity : 0.004 0.045 1449 Dihedral : 16.441 106.361 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 : 2.73 % Allowed : 14.56 % Favored : 82.71 % 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: 1.02 (0.28), residues: 976 helix: 2.33 (0.25), residues: 447 sheet: 0.17 (0.39), residues: 173 loop : -1.27 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 0.00321 / 0.15 ( 8987) covalent geometry : angle 0.56866 / 0.31 (12301) hydrogen bonds : bond 0.05111 / 3.44 ( 440) hydrogen bonds : angle 3.88076 / 2.67 ( 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 201 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 598 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8017 (mt0) REVERT: A 599 GLU cc_start: 0.8131 (tp30) cc_final: 0.7765 (tp30) REVERT: A 644 GLU cc_start: 0.7860 (tp30) cc_final: 0.7633 (mm-30) REVERT: A 728 SER cc_start: 0.8964 (m) cc_final: 0.8729 (m) REVERT: A 744 ARG cc_start: 0.8451 (ttp80) cc_final: 0.7906 (ttm170) REVERT: A 882 HIS cc_start: 0.7818 (t70) cc_final: 0.7480 (t70) REVERT: A 977 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8067 (mtm-85) REVERT: A 988 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8077 (mt0) outliers start: 24 outliers final: 13 residues processed: 185 average time/residue: 0.5366 time to fit residues: 105.1734 Evaluate side-chains 192 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 353 SER 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 Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 988 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 43 optimal weight: 0.0070 chunk 97 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.124161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.108817 restraints weight = 12405.413| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.67 r_work: 0.3418 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1383 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= 0.151 Angle : 0.562 9.424 12301 Z= 0.308 Chirality : 0.043 0.555 1332 Planarity : 0.004 0.042 1449 Dihedral : 16.389 105.654 1506 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.33 % Favored : 94.06 % 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: 2.34 (0.25), residues: 447 sheet: 0.17 (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 0.020 0.001 TYR A 756 PHE 0.018 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 0.00331 / 0.15 ( 8987) covalent geometry : angle 0.56221 / 0.31 (12301) hydrogen bonds : bond 0.05064 / 3.42 ( 440) hydrogen bonds : angle 3.84956 / 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 : 0.320 Fit side-chains REVERT: A 182 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8131 (tt) REVERT: A 598 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: A 599 GLU cc_start: 0.8147 (tp30) cc_final: 0.7763 (tp30) REVERT: A 728 SER cc_start: 0.8964 (m) cc_final: 0.8706 (m) REVERT: A 744 ARG cc_start: 0.8458 (ttp80) cc_final: 0.7847 (ttm170) REVERT: A 841 ASN cc_start: 0.7731 (t0) cc_final: 0.7314 (t0) REVERT: A 882 HIS cc_start: 0.7829 (t70) cc_final: 0.7467 (t70) outliers start: 22 outliers final: 10 residues processed: 189 average time/residue: 0.4936 time to fit residues: 99.0744 Evaluate side-chains 192 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain A residue 677 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 0.1980 chunk 65 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 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: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.124911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109547 restraints weight = 12386.835| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.67 r_work: 0.3429 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1476 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= 0.131 Angle : 0.564 9.647 12301 Z= 0.305 Chirality : 0.043 0.617 1332 Planarity : 0.004 0.040 1449 Dihedral : 16.326 105.239 1506 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.02 % Favored : 94.36 % Rotamer: Outliers : 1.93 % Allowed : 17.18 % Favored : 80.89 % 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: 2.42 (0.25), residues: 449 sheet: 0.15 (0.39), residues: 173 loop : -1.27 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 977 TYR 0.019 0.001 TYR A 974 PHE 0.018 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 0.00272 / 0.13 ( 8987) covalent geometry : angle 0.56359 / 0.30 (12301) hydrogen bonds : bond 0.04635 / 3.12 ( 440) hydrogen bonds : angle 3.79906 / 2.62 ( 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 196 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.202 Fit side-chains REVERT: A 182 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 185 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7293 (mmt90) REVERT: A 248 LEU cc_start: 0.8541 (mp) cc_final: 0.8264 (mt) REVERT: A 598 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: A 599 GLU cc_start: 0.8146 (tp30) cc_final: 0.7781 (tp30) REVERT: A 644 GLU cc_start: 0.7911 (tp30) cc_final: 0.7694 (mm-30) REVERT: A 728 SER cc_start: 0.8963 (m) cc_final: 0.8719 (m) REVERT: A 744 ARG cc_start: 0.8456 (ttp80) cc_final: 0.7859 (ttm170) REVERT: A 841 ASN cc_start: 0.7693 (t0) cc_final: 0.7279 (t0) REVERT: A 882 HIS cc_start: 0.7813 (t70) cc_final: 0.7458 (t70) outliers start: 17 outliers final: 10 residues processed: 185 average time/residue: 0.5700 time to fit residues: 111.8965 Evaluate side-chains 191 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.124678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109362 restraints weight = 12493.466| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.67 r_work: 0.3426 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1531 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= 0.137 Angle : 0.560 9.805 12301 Z= 0.304 Chirality : 0.044 0.646 1332 Planarity : 0.004 0.039 1449 Dihedral : 16.293 105.291 1506 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.92 % Favored : 94.47 % Rotamer: Outliers : 1.93 % Allowed : 17.41 % Favored : 80.66 % 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: 1.08 (0.27), residues: 976 helix: 2.41 (0.25), residues: 449 sheet: 0.13 (0.38), residues: 173 loop : -1.26 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 977 TYR 0.020 0.001 TYR A 555 PHE 0.019 0.001 PHE A 85 TRP 0.010 0.001 TRP A 241 HIS 0.009 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 8987) covalent geometry : angle 0.55959 / 0.30 (12301) hydrogen bonds : bond 0.04664 / 3.14 ( 440) hydrogen bonds : angle 3.79500 / 2.62 ( 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 200 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.215 Fit side-chains REVERT: A 182 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 248 LEU cc_start: 0.8530 (mp) cc_final: 0.8269 (mt) REVERT: A 598 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: A 599 GLU cc_start: 0.8159 (tp30) cc_final: 0.7796 (tp30) REVERT: A 644 GLU cc_start: 0.7906 (tp30) cc_final: 0.7670 (mm-30) REVERT: A 728 SER cc_start: 0.8962 (m) cc_final: 0.8720 (m) REVERT: A 744 ARG cc_start: 0.8459 (ttp80) cc_final: 0.7868 (ttm170) REVERT: A 841 ASN cc_start: 0.7740 (t0) cc_final: 0.7332 (t0) REVERT: A 882 HIS cc_start: 0.7806 (t70) cc_final: 0.7450 (t70) outliers start: 17 outliers final: 11 residues processed: 190 average time/residue: 0.5104 time to fit residues: 102.9490 Evaluate side-chains 194 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 988 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.124863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109535 restraints weight = 12340.746| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.67 r_work: 0.3428 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8987 Z= 0.134 Angle : 0.564 10.080 12301 Z= 0.304 Chirality : 0.044 0.678 1332 Planarity : 0.004 0.039 1449 Dihedral : 16.270 105.348 1506 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.02 % Favored : 94.36 % Rotamer: Outliers : 2.39 % Allowed : 17.29 % Favored : 80.32 % 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: 2.43 (0.25), residues: 449 sheet: -0.02 (0.38), residues: 180 loop : -1.24 (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 0.018 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 0.00280 / 0.13 ( 8987) covalent geometry : angle 0.56381 / 0.30 (12301) hydrogen bonds : bond 0.04553 / 3.06 ( 440) hydrogen bonds : angle 3.77004 / 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 201 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.204 Fit side-chains REVERT: A 182 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 248 LEU cc_start: 0.8531 (mp) cc_final: 0.8287 (mt) REVERT: A 598 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: A 599 GLU cc_start: 0.8153 (tp30) cc_final: 0.7776 (tp30) REVERT: A 728 SER cc_start: 0.8958 (m) cc_final: 0.8704 (m) REVERT: A 744 ARG cc_start: 0.8449 (ttp80) cc_final: 0.7832 (ttm170) REVERT: A 841 ASN cc_start: 0.7765 (t0) cc_final: 0.7377 (t0) REVERT: A 882 HIS cc_start: 0.7805 (t70) cc_final: 0.7437 (t70) outliers start: 21 outliers final: 15 residues processed: 188 average time/residue: 0.5256 time to fit residues: 104.8300 Evaluate side-chains 197 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LYS 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 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 988 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 95 optimal weight: 0.0170 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.125016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109671 restraints weight = 12333.007| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.67 r_work: 0.3433 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8987 Z= 0.131 Angle : 0.561 9.957 12301 Z= 0.303 Chirality : 0.044 0.677 1332 Planarity : 0.004 0.044 1449 Dihedral : 16.244 105.253 1506 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.02 % Favored : 94.36 % Rotamer: Outliers : 2.39 % Allowed : 17.29 % Favored : 80.32 % 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: 1.05 (0.27), residues: 976 helix: 2.42 (0.25), residues: 447 sheet: -0.07 (0.38), residues: 180 loop : -1.22 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.019 0.001 TYR A 756 PHE 0.018 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 0.00273 / 0.13 ( 8987) covalent geometry : angle 0.56055 / 0.30 (12301) hydrogen bonds : bond 0.04470 / 3.00 ( 440) hydrogen bonds : angle 3.77055 / 2.60 ( 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: 21 poor density : 182 time to evaluate : 0.391 Fit side-chains REVERT: A 182 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 219 LYS cc_start: 0.8327 (mmmm) cc_final: 0.8036 (tppt) REVERT: A 248 LEU cc_start: 0.8530 (mp) cc_final: 0.8283 (mt) REVERT: A 598 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: A 599 GLU cc_start: 0.8149 (tp30) cc_final: 0.7780 (tp30) REVERT: A 644 GLU cc_start: 0.7918 (tp30) cc_final: 0.7690 (mm-30) REVERT: A 728 SER cc_start: 0.8961 (m) cc_final: 0.8705 (m) REVERT: A 744 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7815 (ttm170) REVERT: A 841 ASN cc_start: 0.7786 (t0) cc_final: 0.7434 (t0) REVERT: A 882 HIS cc_start: 0.7801 (t70) cc_final: 0.7434 (t70) outliers start: 21 outliers final: 12 residues processed: 190 average time/residue: 0.5726 time to fit residues: 115.4174 Evaluate side-chains 193 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 373 LEU 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 677 ILE 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: 0.8980 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 60 optimal weight: 0.0030 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.125221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109817 restraints weight = 12324.547| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.68 r_work: 0.3435 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8987 Z= 0.129 Angle : 0.570 9.673 12301 Z= 0.304 Chirality : 0.043 0.636 1332 Planarity : 0.004 0.042 1449 Dihedral : 16.229 104.991 1506 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.71 % Favored : 94.67 % Rotamer: Outliers : 1.82 % Allowed : 18.32 % 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: 1.10 (0.28), residues: 976 helix: 2.48 (0.25), residues: 447 sheet: -0.06 (0.38), residues: 180 loop : -1.21 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.019 0.001 TYR A 974 PHE 0.018 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 0.00267 / 0.13 ( 8987) covalent geometry : angle 0.56994 / 0.30 (12301) hydrogen bonds : bond 0.04391 / 2.95 ( 440) hydrogen bonds : angle 3.75703 / 2.60 ( 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 199 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 219 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8002 (tppt) REVERT: A 248 LEU cc_start: 0.8534 (mp) cc_final: 0.8290 (mt) REVERT: A 598 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: A 599 GLU cc_start: 0.8148 (tp30) cc_final: 0.7779 (tp30) REVERT: A 728 SER cc_start: 0.8964 (m) cc_final: 0.8703 (m) REVERT: A 841 ASN cc_start: 0.7787 (t0) cc_final: 0.7486 (t0) REVERT: A 882 HIS cc_start: 0.7811 (t70) cc_final: 0.7442 (t70) outliers start: 16 outliers final: 11 residues processed: 188 average time/residue: 0.5409 time to fit residues: 107.6229 Evaluate side-chains 195 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 677 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 227 GLN A 778 ASN A 841 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.125372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.110049 restraints weight = 12389.788| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.68 r_work: 0.3439 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8987 Z= 0.125 Angle : 0.558 9.377 12301 Z= 0.299 Chirality : 0.042 0.567 1332 Planarity : 0.004 0.040 1449 Dihedral : 16.207 104.514 1506 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.61 % Favored : 94.77 % Rotamer: Outliers : 1.59 % Allowed : 18.89 % Favored : 79.52 % 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: 1.10 (0.28), residues: 976 helix: 2.50 (0.25), residues: 446 sheet: -0.09 (0.38), residues: 180 loop : -1.21 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.018 0.001 TYR A 756 PHE 0.018 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 0.00257 / 0.12 ( 8987) covalent geometry : angle 0.55825 / 0.30 (12301) hydrogen bonds : bond 0.04268 / 2.86 ( 440) hydrogen bonds : angle 3.75912 / 2.59 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3443.73 seconds wall clock time: 59 minutes 4.97 seconds (3544.97 seconds total)