Starting phenix.real_space_refine on Wed Sep 17 12:35:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywi_39634/09_2025/8ywi_39634.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywi_39634/09_2025/8ywi_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_39634/09_2025/8ywi_39634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywi_39634/09_2025/8ywi_39634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ywi_39634/09_2025/8ywi_39634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywi_39634/09_2025/8ywi_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-2.0-5805/lib/python3.9/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: 2.06, per 1000 atoms: 0.24 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: 0.82 Conformation dependent library (CDL) restraints added in 324.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.06 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: 1.76 Time building geometry restraints manager: 1.07 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=" C5 TTP T1101 " pdb=" C6 TTP T1101 " ideal model delta sigma weight residual 1.390 1.342 0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C4 TTP T1101 " pdb=" N3 TTP T1101 " ideal model delta sigma weight residual 1.337 1.383 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C4 TTP T1101 " pdb=" C5 TTP T1101 " ideal model delta sigma weight residual 1.487 1.445 0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C6 TTP T1101 " pdb=" N1 TTP T1101 " ideal model delta sigma weight residual 1.337 1.379 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C2 TTP T1101 " pdb=" N3 TTP T1101 " ideal model delta sigma weight residual 1.337 1.373 -0.036 2.00e-02 2.50e+03 3.18e+00 ... (remaining 8982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 12091 2.12 - 4.25: 171 4.25 - 6.37: 25 6.37 - 8.49: 7 8.49 - 10.61: 7 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=" N VAL A 194 " pdb=" CA VAL A 194 " pdb=" CB VAL A 194 " ideal model delta sigma weight residual 111.23 117.17 -5.94 1.65e+00 3.67e-01 1.29e+01 angle pdb=" O1B TTP T1101 " pdb=" PB TTP T1101 " pdb=" O2B TTP T1101 " ideal model delta sigma weight residual 109.50 119.90 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C2' TTP T1101 " pdb=" C3' TTP T1101 " pdb=" C4' TTP T1101 " ideal model delta sigma weight residual 111.00 101.07 9.93 3.00e+00 1.11e-01 1.10e+01 ... (remaining 12296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.69: 4982 27.69 - 55.37: 338 55.37 - 83.05: 21 83.05 - 110.74: 3 110.74 - 138.42: 3 Dihedral angle restraints: 5347 sinusoidal: 2440 harmonic: 2907 Sorted by residual: dihedral pdb=" C2 TTP T1101 " pdb=" C1' TTP T1101 " pdb=" N1 TTP T1101 " pdb=" O4' TTP T1101 " ideal model delta sinusoidal sigma weight residual 301.68 163.26 138.42 1 2.00e+01 2.50e-03 4.20e+01 dihedral pdb=" O3A TTP T1101 " pdb=" O3B TTP T1101 " pdb=" PB TTP T1101 " pdb=" PG TTP T1101 " ideal model delta sinusoidal sigma weight residual 179.98 -48.45 -131.57 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O5' TTP T1101 " pdb=" O3A TTP T1101 " pdb=" PA TTP T1101 " pdb=" PB TTP T1101 " ideal model delta sinusoidal sigma weight residual 180.02 54.77 125.25 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 5344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1279 0.096 - 0.192: 51 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: 3.220 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8987 Z= 0.158 Angle : 0.654 10.613 12301 Z= 0.340 Chirality : 0.042 0.480 1332 Planarity : 0.005 0.094 1449 Dihedral : 16.773 138.423 3475 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 aren 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 covalent geometry : bond 0.00334 ( 8987) covalent geometry : angle 0.65413 (12301) hydrogen bonds : bond 0.13802 ( 440) hydrogen bonds : angle 4.77211 ( 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 : 0.342 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: 0.6565 time to fit residues: 136.7973 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 : 0.325 ------------------------------------------------------------------------------- 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: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 29 ASN 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 = 0.3724 r_free = 0.3724 target = 0.124069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108760 restraints weight = 12443.208| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.66 r_work: 0.3416 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1072 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= 0.167 Angle : 0.594 10.519 12301 Z= 0.316 Chirality : 0.043 0.468 1332 Planarity : 0.005 0.065 1449 Dihedral : 16.517 137.123 1484 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.43 % Favored : 93.95 % Rotamer: Outliers : 1.93 % Allowed : 11.15 % Favored : 86.92 % 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 aren not related in a simple way. whole: 0.99 (0.28), residues: 976 helix: 2.25 (0.25), residues: 447 sheet: 0.24 (0.40), residues: 173 loop : -1.27 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 744 TYR 0.021 0.001 TYR A 756 PHE 0.016 0.002 PHE A 85 TRP 0.013 0.001 TRP A 325 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8987) covalent geometry : angle 0.59442 (12301) hydrogen bonds : bond 0.05291 ( 440) hydrogen bonds : angle 3.92944 ( 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 198 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 248 LEU cc_start: 0.8524 (mt) cc_final: 0.8305 (mp) REVERT: A 598 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: A 599 GLU cc_start: 0.8132 (tp30) cc_final: 0.7742 (tp30) REVERT: A 644 GLU cc_start: 0.7914 (tp30) cc_final: 0.7620 (mm-30) REVERT: A 728 SER cc_start: 0.8965 (m) cc_final: 0.8694 (m) REVERT: A 744 ARG cc_start: 0.8444 (ttp80) cc_final: 0.7833 (ttm170) REVERT: A 841 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7542 (t0) REVERT: A 882 HIS cc_start: 0.7864 (t70) cc_final: 0.7505 (t70) REVERT: A 974 TYR cc_start: 0.8116 (t80) cc_final: 0.7586 (t80) REVERT: A 988 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8082 (mt0) outliers start: 17 outliers final: 11 residues processed: 186 average time/residue: 0.6800 time to fit residues: 133.4042 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 : 0.328 ------------------------------------------------------------------------------- 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 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 919 SER 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: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3715 r_free = 0.3715 target = 0.123311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107993 restraints weight = 12347.167| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.66 r_work: 0.3407 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1305 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= 0.174 Angle : 0.591 10.104 12301 Z= 0.314 Chirality : 0.043 0.503 1332 Planarity : 0.004 0.050 1449 Dihedral : 16.406 136.600 1482 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.23 % Favored : 94.16 % Rotamer: Outliers : 2.62 % Allowed : 13.42 % Favored : 83.96 % 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 aren not related in a simple way. whole: 0.97 (0.27), residues: 976 helix: 2.28 (0.25), residues: 445 sheet: 0.20 (0.39), residues: 173 loop : -1.29 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 978 TYR 0.020 0.001 TYR A 756 PHE 0.013 0.001 PHE A 85 TRP 0.011 0.001 TRP A 325 HIS 0.011 0.001 HIS A 873 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8987) covalent geometry : angle 0.59105 (12301) hydrogen bonds : bond 0.05354 ( 440) hydrogen bonds : angle 3.89683 ( 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: 23 poor density : 181 time to evaluate : 0.333 Fit side-chains REVERT: A 146 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8432 (m) REVERT: A 182 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 248 LEU cc_start: 0.8517 (mt) cc_final: 0.8313 (mp) REVERT: A 598 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: A 599 GLU cc_start: 0.8129 (tp30) cc_final: 0.7746 (tp30) REVERT: A 644 GLU cc_start: 0.7912 (tp30) cc_final: 0.7656 (mm-30) REVERT: A 728 SER cc_start: 0.8964 (m) cc_final: 0.8695 (m) REVERT: A 744 ARG cc_start: 0.8453 (ttp80) cc_final: 0.7818 (ttm170) REVERT: A 882 HIS cc_start: 0.7838 (t70) cc_final: 0.7471 (t70) REVERT: A 988 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8097 (mt0) outliers start: 23 outliers final: 12 residues processed: 190 average time/residue: 0.6504 time to fit residues: 130.7492 Evaluate side-chains 194 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 167 THR 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 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 688 THR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 919 SER 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: 0.6980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 778 ASN A 841 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108769 restraints weight = 12489.755| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.67 r_work: 0.3419 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1444 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= 0.145 Angle : 0.569 9.604 12301 Z= 0.302 Chirality : 0.042 0.518 1332 Planarity : 0.004 0.043 1449 Dihedral : 16.269 137.259 1482 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.12 % Favored : 94.26 % Rotamer: Outliers : 2.84 % Allowed : 14.68 % Favored : 82.48 % 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 aren not related in a simple way. whole: 1.03 (0.27), residues: 976 helix: 2.33 (0.25), residues: 449 sheet: 0.18 (0.39), residues: 173 loop : -1.28 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 977 TYR 0.018 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 covalent geometry : bond 0.00328 ( 8987) covalent geometry : angle 0.56862 (12301) hydrogen bonds : bond 0.04810 ( 440) hydrogen bonds : angle 3.81788 ( 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 207 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.341 Fit side-chains REVERT: A 182 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8136 (tt) REVERT: A 248 LEU cc_start: 0.8532 (mt) cc_final: 0.8331 (mp) REVERT: A 598 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: A 599 GLU cc_start: 0.8134 (tp30) cc_final: 0.7760 (tp30) REVERT: A 644 GLU cc_start: 0.7869 (tp30) cc_final: 0.7588 (mm-30) REVERT: A 728 SER cc_start: 0.8954 (m) cc_final: 0.8695 (m) REVERT: A 744 ARG cc_start: 0.8454 (ttp80) cc_final: 0.7820 (ttm170) REVERT: A 841 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7486 (t0) REVERT: A 875 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7843 (ttm170) REVERT: A 882 HIS cc_start: 0.7837 (t70) cc_final: 0.7474 (t70) outliers start: 25 outliers final: 12 residues processed: 191 average time/residue: 0.6574 time to fit residues: 132.8287 Evaluate side-chains 194 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 LEU 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 592 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 919 SER 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: 2.9990 chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 227 GLN 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 = 0.3717 r_free = 0.3717 target = 0.123458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108140 restraints weight = 12424.385| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.65 r_work: 0.3410 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1510 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= 0.165 Angle : 0.582 9.582 12301 Z= 0.309 Chirality : 0.043 0.556 1332 Planarity : 0.004 0.042 1449 Dihedral : 16.247 137.697 1482 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.53 % Favored : 93.85 % Rotamer: Outliers : 2.96 % Allowed : 15.47 % Favored : 81.57 % 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 aren not related in a simple way. whole: 0.99 (0.27), residues: 976 helix: 2.32 (0.25), residues: 447 sheet: 0.14 (0.39), residues: 173 loop : -1.30 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 977 TYR 0.019 0.001 TYR A 555 PHE 0.015 0.001 PHE A 85 TRP 0.010 0.001 TRP A 241 HIS 0.011 0.001 HIS A 873 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8987) covalent geometry : angle 0.58197 (12301) hydrogen bonds : bond 0.05092 ( 440) hydrogen bonds : angle 3.84367 ( 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 212 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 598 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: A 599 GLU cc_start: 0.8131 (tp30) cc_final: 0.7799 (tp30) REVERT: A 644 GLU cc_start: 0.7847 (tp30) cc_final: 0.7613 (mm-30) REVERT: A 728 SER cc_start: 0.8955 (m) cc_final: 0.8723 (m) REVERT: A 744 ARG cc_start: 0.8476 (ttp80) cc_final: 0.7908 (ttm170) REVERT: A 882 HIS cc_start: 0.7825 (t70) cc_final: 0.7474 (t70) outliers start: 26 outliers final: 13 residues processed: 196 average time/residue: 0.6421 time to fit residues: 133.3324 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 : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 LEU 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 592 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 932 LYS Chi-restraints excluded: chain A residue 988 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3722 r_free = 0.3722 target = 0.123823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108517 restraints weight = 12373.092| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.65 r_work: 0.3415 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1602 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 : 0.575 9.764 12301 Z= 0.304 Chirality : 0.043 0.578 1332 Planarity : 0.004 0.040 1449 Dihedral : 16.211 138.240 1482 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.23 % Favored : 94.16 % Rotamer: Outliers : 2.73 % Allowed : 16.95 % 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 aren not related in a simple way. whole: 1.01 (0.27), residues: 976 helix: 2.36 (0.25), residues: 449 sheet: 0.11 (0.39), residues: 173 loop : -1.32 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 977 TYR 0.018 0.001 TYR A 555 PHE 0.016 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 covalent geometry : bond 0.00342 ( 8987) covalent geometry : angle 0.57462 (12301) hydrogen bonds : bond 0.04822 ( 440) hydrogen bonds : angle 3.80645 ( 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 214 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.331 Fit side-chains REVERT: A 167 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8257 (m) REVERT: A 182 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8189 (tt) REVERT: A 598 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: A 599 GLU cc_start: 0.8144 (tp30) cc_final: 0.7808 (tp30) REVERT: A 644 GLU cc_start: 0.7828 (tp30) cc_final: 0.7582 (mm-30) REVERT: A 728 SER cc_start: 0.8950 (m) cc_final: 0.8721 (m) REVERT: A 744 ARG cc_start: 0.8462 (ttp80) cc_final: 0.7919 (ttm170) REVERT: A 882 HIS cc_start: 0.7799 (t70) cc_final: 0.7455 (t70) REVERT: A 978 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7577 (mpp-170) outliers start: 24 outliers final: 13 residues processed: 198 average time/residue: 0.6335 time to fit residues: 132.9222 Evaluate side-chains 204 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 237 MET 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 919 SER Chi-restraints excluded: chain A residue 978 ARG 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: 0.0980 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3719 r_free = 0.3719 target = 0.123611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.108273 restraints weight = 12470.153| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.66 r_work: 0.3412 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1655 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= 0.153 Angle : 0.582 9.694 12301 Z= 0.307 Chirality : 0.043 0.600 1332 Planarity : 0.004 0.039 1449 Dihedral : 16.203 138.478 1482 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.92 % Favored : 94.47 % Rotamer: Outliers : 3.64 % Allowed : 16.95 % Favored : 79.41 % 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 aren not related in a simple way. whole: 1.02 (0.28), residues: 976 helix: 2.41 (0.25), residues: 447 sheet: -0.02 (0.38), residues: 180 loop : -1.30 (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 555 PHE 0.013 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 covalent geometry : bond 0.00347 ( 8987) covalent geometry : angle 0.58165 (12301) hydrogen bonds : bond 0.04837 ( 440) hydrogen bonds : angle 3.79414 ( 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 218 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.349 Fit side-chains REVERT: A 182 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 598 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: A 599 GLU cc_start: 0.8134 (tp30) cc_final: 0.7803 (tp30) REVERT: A 644 GLU cc_start: 0.7831 (tp30) cc_final: 0.7589 (mm-30) REVERT: A 728 SER cc_start: 0.8940 (m) cc_final: 0.8716 (m) REVERT: A 744 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7907 (ttm170) REVERT: A 882 HIS cc_start: 0.7814 (t70) cc_final: 0.7469 (t70) REVERT: A 973 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6790 (tm-30) REVERT: A 974 TYR cc_start: 0.8338 (t80) cc_final: 0.7521 (t80) REVERT: A 977 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8122 (ttm-80) REVERT: A 978 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7585 (mpp-170) outliers start: 32 outliers final: 15 residues processed: 199 average time/residue: 0.6137 time to fit residues: 129.5627 Evaluate side-chains 203 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 167 THR 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 237 MET 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 592 LYS 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 919 SER Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 978 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3725 r_free = 0.3725 target = 0.123915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108726 restraints weight = 12364.704| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.66 r_work: 0.3420 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 0.031 8987 Z= 0.144 Angle : 0.583 9.645 12301 Z= 0.306 Chirality : 0.043 0.593 1332 Planarity : 0.004 0.038 1449 Dihedral : 16.188 138.861 1482 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.92 % Favored : 94.47 % Rotamer: Outliers : 2.62 % Allowed : 18.32 % Favored : 79.07 % 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 aren not related in a simple way. whole: 1.01 (0.28), residues: 976 helix: 2.43 (0.25), residues: 445 sheet: -0.07 (0.38), residues: 180 loop : -1.29 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.017 0.001 TYR A 555 PHE 0.012 0.001 PHE A 85 TRP 0.010 0.001 TRP A 241 HIS 0.006 0.001 HIS A 873 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8987) covalent geometry : angle 0.58279 (12301) hydrogen bonds : bond 0.04648 ( 440) hydrogen bonds : angle 3.78405 ( 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 206 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.355 Fit side-chains REVERT: A 167 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8282 (m) REVERT: A 182 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8210 (tt) REVERT: A 598 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: A 599 GLU cc_start: 0.8152 (tp30) cc_final: 0.7815 (tp30) REVERT: A 644 GLU cc_start: 0.7765 (tp30) cc_final: 0.7541 (mm-30) REVERT: A 728 SER cc_start: 0.8926 (m) cc_final: 0.8703 (m) REVERT: A 744 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7904 (ttm170) REVERT: A 882 HIS cc_start: 0.7804 (t70) cc_final: 0.7453 (t70) REVERT: A 973 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6766 (tt0) REVERT: A 974 TYR cc_start: 0.8294 (t80) cc_final: 0.7472 (t80) REVERT: A 978 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7577 (mpp-170) outliers start: 23 outliers final: 13 residues processed: 192 average time/residue: 0.6526 time to fit residues: 132.2609 Evaluate side-chains 199 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 167 THR 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 237 MET 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 750 SER Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 978 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3726 r_free = 0.3726 target = 0.124058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.108805 restraints weight = 12376.646| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.68 r_work: 0.3423 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1746 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 : 0.598 9.537 12301 Z= 0.312 Chirality : 0.042 0.561 1332 Planarity : 0.004 0.048 1449 Dihedral : 16.191 139.093 1482 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.12 % Favored : 94.26 % Rotamer: Outliers : 2.84 % Allowed : 18.09 % Favored : 79.07 % 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 aren not related in a simple way. whole: 0.99 (0.28), residues: 976 helix: 2.42 (0.25), residues: 445 sheet: -0.11 (0.38), residues: 180 loop : -1.30 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.017 0.001 TYR A 555 PHE 0.012 0.001 PHE A 85 TRP 0.010 0.001 TRP A 241 HIS 0.006 0.001 HIS A 873 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8987) covalent geometry : angle 0.59819 (12301) hydrogen bonds : bond 0.04691 ( 440) hydrogen bonds : angle 3.81259 ( 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 207 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.349 Fit side-chains REVERT: A 167 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8326 (m) REVERT: A 182 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 598 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: A 599 GLU cc_start: 0.8151 (tp30) cc_final: 0.7788 (tp30) REVERT: A 644 GLU cc_start: 0.7811 (tp30) cc_final: 0.7581 (mm-30) REVERT: A 728 SER cc_start: 0.8941 (m) cc_final: 0.8700 (m) REVERT: A 744 ARG cc_start: 0.8436 (ttp80) cc_final: 0.7847 (ttm170) REVERT: A 825 PRO cc_start: 0.8977 (Cg_endo) cc_final: 0.8737 (Cg_exo) REVERT: A 882 HIS cc_start: 0.7802 (t70) cc_final: 0.7439 (t70) REVERT: A 974 TYR cc_start: 0.8304 (t80) cc_final: 0.7461 (t80) REVERT: A 978 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7546 (mpp-170) outliers start: 25 outliers final: 14 residues processed: 191 average time/residue: 0.6568 time to fit residues: 132.3969 Evaluate side-chains 200 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 167 THR 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 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 750 SER Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 978 ARG 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: 0.0370 chunk 53 optimal weight: 0.0570 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3738 r_free = 0.3738 target = 0.125016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109703 restraints weight = 12372.162| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.69 r_work: 0.3436 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1795 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= 0.132 Angle : 0.594 9.438 12301 Z= 0.308 Chirality : 0.041 0.483 1332 Planarity : 0.004 0.045 1449 Dihedral : 16.152 139.177 1482 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.92 % Favored : 94.47 % Rotamer: Outliers : 1.93 % Allowed : 19.11 % Favored : 78.95 % 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 aren not related in a simple way. whole: 0.98 (0.28), residues: 976 helix: 2.43 (0.25), residues: 445 sheet: -0.19 (0.38), residues: 180 loop : -1.29 (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 0.012 0.001 PHE A 85 TRP 0.011 0.001 TRP A 241 HIS 0.005 0.001 HIS A 873 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8987) covalent geometry : angle 0.59402 (12301) hydrogen bonds : bond 0.04325 ( 440) hydrogen bonds : angle 3.77149 ( 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 198 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.393 Fit side-chains REVERT: A 182 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 598 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: A 599 GLU cc_start: 0.8170 (tp30) cc_final: 0.7808 (tp30) REVERT: A 644 GLU cc_start: 0.7772 (tp30) cc_final: 0.7544 (mm-30) REVERT: A 705 ASP cc_start: 0.7923 (t0) cc_final: 0.7696 (t0) REVERT: A 728 SER cc_start: 0.8946 (m) cc_final: 0.8696 (m) REVERT: A 825 PRO cc_start: 0.8984 (Cg_endo) cc_final: 0.8766 (Cg_exo) REVERT: A 882 HIS cc_start: 0.7796 (t70) cc_final: 0.7433 (t70) outliers start: 17 outliers final: 15 residues processed: 189 average time/residue: 0.6558 time to fit residues: 130.9632 Evaluate side-chains 193 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 167 THR 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 373 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 919 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3735 r_free = 0.3735 target = 0.124826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109593 restraints weight = 12415.530| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.68 r_work: 0.3434 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 8987 Z= 0.225 Angle : 0.935 59.200 12301 Z= 0.550 Chirality : 0.043 0.442 1332 Planarity : 0.004 0.066 1449 Dihedral : 16.166 139.163 1482 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.82 % Favored : 94.47 % Rotamer: Outliers : 1.93 % Allowed : 19.11 % Favored : 78.95 % Cbeta Deviations : 0.11 % 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 aren not related in a simple way. whole: 0.97 (0.28), residues: 976 helix: 2.42 (0.25), residues: 445 sheet: -0.19 (0.38), residues: 180 loop : -1.30 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.015 0.001 TYR A 555 PHE 0.012 0.001 PHE A 85 TRP 0.010 0.001 TRP A 241 HIS 0.006 0.001 HIS A 873 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8987) covalent geometry : angle 0.93496 (12301) hydrogen bonds : bond 0.04361 ( 440) hydrogen bonds : angle 3.76987 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.47 seconds wall clock time: 68 minutes 10.44 seconds (4090.44 seconds total)