Starting phenix.real_space_refine on Fri Sep 11 18:54:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gjz_0012/09_2026/6gjz_0012.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gjz_0012/09_2026/6gjz_0012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2026/6gjz_0012.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2026/6gjz_0012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2026/6gjz_0012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2026/6gjz_0012.map" model { file = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2026/6gjz_0012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2026/6gjz_0012.cif" } resolution = 4.06 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= 0.009 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 31 5.49 5 S 35 5.16 5 C 3744 2.51 5 N 1063 2.21 5 O 1227 1.98 5 H 4402 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10503 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 9874 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 661} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "X" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 308 Classifications: {'RNAv2': 14} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 289 Classifications: {'RNAv2': 14} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 11} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8332 SG CYS A 907 77.322 30.711 39.800 1.00183.18 S ATOM 8379 SG CYS A 910 81.069 29.924 39.936 1.00185.36 S ATOM 9041 SG CYS A 962 79.747 30.998 43.514 1.00195.13 S ATOM 9060 SG CYS A 964 79.539 33.780 41.219 1.00187.69 S Time building chain proxies: 1.98, per 1000 atoms: 0.19 Number of scatterers: 10503 At special positions: 0 Unit cell: (100.58, 86.67, 69.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 35 16.00 P 31 15.00 O 1227 8.00 N 1063 7.00 C 3744 6.00 H 4402 1.00 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: 0.87 Conformation dependent library (CDL) restraints added in 221.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " Number of angles added : 6 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 52.6% alpha, 9.4% beta 14 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.744A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 367 through 377 removed outlier: 4.052A pdb=" N GLU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.910A pdb=" N TYR A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 removed outlier: 3.594A pdb=" N VAL A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.702A pdb=" N GLU A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 456 through 474 Processing helix chain 'A' and resid 499 through 514 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.973A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.537A pdb=" N LYS A 554 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 Processing helix chain 'A' and resid 598 through 618 removed outlier: 3.657A pdb=" N LYS A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.782A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 692 removed outlier: 3.724A pdb=" N ASP A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 4.169A pdb=" N GLU A 697 " --> pdb=" O PRO A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 716 removed outlier: 3.901A pdb=" N ILE A 702 " --> pdb=" O ASN A 698 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.911A pdb=" N THR A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 747 removed outlier: 3.934A pdb=" N ALA A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 812 through 821 Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.765A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 890 removed outlier: 4.049A pdb=" N LYS A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 939 removed outlier: 3.619A pdb=" N LEU A 938 " --> pdb=" O GLU A 934 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR A 939 " --> pdb=" O PHE A 935 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.399A pdb=" N ILE A 326 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR A 489 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 328 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 441 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 488 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 443 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE A 361 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASP A 444 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU A 363 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 414 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 542 removed outlier: 3.507A pdb=" N THR A 834 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 751 through 754 removed outlier: 6.791A pdb=" N HIS A 752 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 722 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 912 through 916 removed outlier: 4.026A pdb=" N MET A 912 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 905 " --> pdb=" O VAL A 914 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=AA6, first strand: chain 'A' and resid 940 through 942 removed outlier: 3.688A pdb=" N GLU A 959 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 960 " --> pdb=" O TRP A 968 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 970 " --> pdb=" O CYS A 981 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 4391 1.02 - 1.22: 17 1.22 - 1.42: 2595 1.42 - 1.62: 3597 1.62 - 1.82: 58 Bond restraints: 10658 Sorted by residual: bond pdb=" O3A ANP A1102 " pdb=" PB ANP A1102 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" N3B ANP A1102 " pdb=" PG ANP A1102 " ideal model delta sigma weight residual 1.795 1.685 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" O5' ANP A1102 " pdb=" PA ANP A1102 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" CD ARG A 824 " pdb=" NE ARG A 824 " ideal model delta sigma weight residual 1.458 1.410 0.048 1.40e-02 5.10e+03 1.16e+01 bond pdb=" C SER A 995 " pdb=" O SER A 995 " ideal model delta sigma weight residual 1.233 1.219 0.014 4.80e-03 4.34e+04 7.96e+00 ... (remaining 10653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.04: 18601 11.04 - 22.07: 7 22.07 - 33.11: 0 33.11 - 44.14: 0 44.14 - 55.18: 14 Bond angle restraints: 18622 Sorted by residual: angle pdb=" C LYS A 884 " pdb=" N LYS A 885 " pdb=" H LYS A 885 " ideal model delta sigma weight residual 124.88 69.70 55.18 3.00e+00 1.11e-01 3.38e+02 angle pdb=" C MET A 886 " pdb=" N LYS A 887 " pdb=" H LYS A 887 " ideal model delta sigma weight residual 124.96 70.80 54.16 3.00e+00 1.11e-01 3.26e+02 angle pdb=" C LYS A 451 " pdb=" N GLU A 452 " pdb=" H GLU A 452 " ideal model delta sigma weight residual 124.38 70.51 53.87 3.00e+00 1.11e-01 3.22e+02 angle pdb=" CA LYS A 887 " pdb=" N LYS A 887 " pdb=" H LYS A 887 " ideal model delta sigma weight residual 114.66 61.11 53.55 3.00e+00 1.11e-01 3.19e+02 angle pdb=" CA LYS A 885 " pdb=" N LYS A 885 " pdb=" H LYS A 885 " ideal model delta sigma weight residual 114.58 61.37 53.21 3.00e+00 1.11e-01 3.15e+02 ... (remaining 18617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4983 17.46 - 34.91: 195 34.91 - 52.37: 55 52.37 - 69.83: 12 69.83 - 87.28: 6 Dihedral angle restraints: 5251 sinusoidal: 2985 harmonic: 2266 Sorted by residual: dihedral pdb=" CA VAL A 454 " pdb=" C VAL A 454 " pdb=" N TYR A 455 " pdb=" CA TYR A 455 " ideal model delta harmonic sigma weight residual 180.00 92.72 87.28 0 5.00e+00 4.00e-02 3.05e+02 dihedral pdb=" CA GLU A 548 " pdb=" C GLU A 548 " pdb=" N ASN A 549 " pdb=" CA ASN A 549 " ideal model delta harmonic sigma weight residual 180.00 -143.68 -36.32 0 5.00e+00 4.00e-02 5.28e+01 dihedral pdb=" CA PRO A 550 " pdb=" C PRO A 550 " pdb=" N PHE A 551 " pdb=" CA PHE A 551 " ideal model delta harmonic sigma weight residual -180.00 -145.10 -34.90 0 5.00e+00 4.00e-02 4.87e+01 ... (remaining 5248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 707 0.053 - 0.107: 206 0.107 - 0.160: 49 0.160 - 0.213: 22 0.213 - 0.266: 3 Chirality restraints: 987 Sorted by residual: chirality pdb=" C3' ANP A1102 " pdb=" C2' ANP A1102 " pdb=" C4' ANP A1102 " pdb=" O3' ANP A1102 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE A 984 " pdb=" CA ILE A 984 " pdb=" CG1 ILE A 984 " pdb=" CG2 ILE A 984 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" P C X 5 " pdb=" OP1 C X 5 " pdb=" OP2 C X 5 " pdb=" O5' C X 5 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 984 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 455 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C TYR A 455 " -0.062 2.00e-02 2.50e+03 pdb=" O TYR A 455 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A 456 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 457 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" N ILE A 458 " 0.044 2.00e-02 2.50e+03 pdb=" CA ILE A 458 " -0.011 2.00e-02 2.50e+03 pdb=" H ILE A 458 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 344 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C THR A 344 " 0.038 2.00e-02 2.50e+03 pdb=" O THR A 344 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 345 " -0.013 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 350 2.18 - 2.78: 19115 2.78 - 3.39: 25275 3.39 - 3.99: 34157 3.99 - 4.60: 54229 Nonbonded interactions: 133126 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.571 1.816 nonbonded pdb=" H VAL A 888 " pdb=" HA VAL A 888 " model vdw 1.604 1.816 nonbonded pdb=" H GLY A 795 " pdb=" HA3 GLY A 795 " model vdw 1.631 1.816 nonbonded pdb=" H LYS A 887 " pdb=" HA LYS A 887 " model vdw 1.633 1.816 nonbonded pdb=" H GLU A 794 " pdb=" HA GLU A 794 " model vdw 1.647 1.816 ... (remaining 133121 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 group one per residue 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.090 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.014 0.612 6260 Z= 0.637 Angle : 1.190 25.798 8559 Z= 0.620 Chirality : 0.058 0.266 987 Planarity : 0.006 0.049 979 Dihedral : 11.156 87.282 2487 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.83 % Favored : 88.87 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -4.09 (0.27), residues: 674 helix: -1.53 (0.24), residues: 327 sheet: -3.18 (0.47), residues: 85 loop : -4.07 (0.30), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 619 TYR 0.024 0.003 TYR A 408 PHE 0.016 0.002 PHE A 517 TRP 0.011 0.003 TRP A1003 HIS 0.012 0.003 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.01152 / 0.58 ( 6256) covalent geometry : angle 1.13072 / 0.62 ( 8553) hydrogen bonds : bond 0.13733 / 9.71 ( 294) hydrogen bonds : angle 6.67237 / 4.66 ( 821) metal coordination : bond 0.30719 / 16.16 ( 4) metal coordination : angle 14.05327 / 7.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.8615 (t70) cc_final: 0.7573 (t70) REVERT: A 520 LYS cc_start: 0.9324 (mmmt) cc_final: 0.9013 (mmmt) REVERT: A 580 GLU cc_start: 0.9384 (tt0) cc_final: 0.9025 (tm-30) REVERT: A 603 GLU cc_start: 0.9287 (tt0) cc_final: 0.8726 (tm-30) REVERT: A 607 LYS cc_start: 0.9478 (mmtt) cc_final: 0.9069 (mmmm) REVERT: A 612 LEU cc_start: 0.9450 (mt) cc_final: 0.9189 (mt) REVERT: A 816 MET cc_start: 0.8771 (ttt) cc_final: 0.8559 (ttt) REVERT: A 874 LEU cc_start: 0.9615 (mt) cc_final: 0.9414 (mm) REVERT: A 884 LYS cc_start: 0.9074 (tptp) cc_final: 0.8629 (tppt) REVERT: A 924 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8117 (mt-10) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1542 time to fit residues: 35.5307 Evaluate side-chains 108 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.0060 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 GLN A 457 ASN A 531 HIS A 563 GLN A 577 GLN A 759 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.071745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.058038 restraints weight = 62651.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.061088 restraints weight = 26157.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062976 restraints weight = 14812.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064187 restraints weight = 10216.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064948 restraints weight = 7924.815| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6260 Z= 0.148 Angle : 0.778 21.283 8559 Z= 0.412 Chirality : 0.042 0.190 987 Planarity : 0.004 0.048 979 Dihedral : 10.456 80.369 1062 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.33 % Allowed : 0.99 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.31 (0.31), residues: 674 helix: 0.43 (0.28), residues: 322 sheet: -2.98 (0.49), residues: 86 loop : -3.61 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 619 TYR 0.013 0.001 TYR A 342 PHE 0.008 0.001 PHE A 401 TRP 0.006 0.001 TRP A 737 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 6256) covalent geometry : angle 0.77280 / 0.41 ( 8553) hydrogen bonds : bond 0.04356 / 2.86 ( 294) hydrogen bonds : angle 4.66245 / 3.17 ( 821) metal coordination : bond 0.00333 / 0.17 ( 4) metal coordination : angle 3.49731 / 1.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 GLU cc_start: 0.8570 (mp0) cc_final: 0.7936 (mp0) REVERT: A 459 MET cc_start: 0.9327 (mmm) cc_final: 0.9018 (mmm) REVERT: A 488 LEU cc_start: 0.9129 (mp) cc_final: 0.8804 (tt) REVERT: A 580 GLU cc_start: 0.9370 (tt0) cc_final: 0.8750 (tm-30) REVERT: A 603 GLU cc_start: 0.9198 (tt0) cc_final: 0.8427 (tm-30) REVERT: A 607 LYS cc_start: 0.9505 (mmtt) cc_final: 0.9207 (mmtm) REVERT: A 790 THR cc_start: 0.9064 (p) cc_final: 0.8603 (p) REVERT: A 884 LYS cc_start: 0.8996 (tptp) cc_final: 0.8506 (tppt) REVERT: A 924 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 926 MET cc_start: 0.8531 (mtp) cc_final: 0.8186 (ptp) REVERT: A 931 MET cc_start: 0.7429 (ppp) cc_final: 0.7151 (ppp) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.1476 time to fit residues: 25.0006 Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 ASN A 531 HIS A 759 HIS A 986 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.068298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.054711 restraints weight = 65168.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057531 restraints weight = 28108.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059277 restraints weight = 16337.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.060438 restraints weight = 11468.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061092 restraints weight = 9012.289| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6260 Z= 0.205 Angle : 0.818 21.062 8559 Z= 0.424 Chirality : 0.043 0.236 987 Planarity : 0.004 0.038 979 Dihedral : 10.547 87.037 1062 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.79 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.50 (0.32), residues: 674 helix: 1.13 (0.28), residues: 332 sheet: -2.74 (0.48), residues: 86 loop : -3.36 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 619 TYR 0.013 0.002 TYR A 455 PHE 0.015 0.001 PHE A 401 TRP 0.008 0.001 TRP A 737 HIS 0.006 0.002 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 ( 6256) covalent geometry : angle 0.81542 / 0.42 ( 8553) hydrogen bonds : bond 0.03850 / 2.57 ( 294) hydrogen bonds : angle 4.37998 / 3.00 ( 821) metal coordination : bond 0.00552 / 0.28 ( 4) metal coordination : angle 2.69453 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ILE cc_start: 0.9054 (tt) cc_final: 0.8798 (mt) REVERT: A 419 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 445 GLU cc_start: 0.8486 (mp0) cc_final: 0.8265 (mp0) REVERT: A 459 MET cc_start: 0.9299 (mmm) cc_final: 0.8995 (mmm) REVERT: A 488 LEU cc_start: 0.8928 (mp) cc_final: 0.8711 (tt) REVERT: A 535 GLU cc_start: 0.8206 (mp0) cc_final: 0.7822 (mp0) REVERT: A 580 GLU cc_start: 0.9398 (tt0) cc_final: 0.8869 (tm-30) REVERT: A 586 MET cc_start: 0.9267 (tpp) cc_final: 0.8977 (tpp) REVERT: A 603 GLU cc_start: 0.9079 (tt0) cc_final: 0.8594 (tm-30) REVERT: A 607 LYS cc_start: 0.9574 (mmtt) cc_final: 0.9331 (mmtm) REVERT: A 739 MET cc_start: 0.8465 (ptt) cc_final: 0.8173 (ppp) REVERT: A 884 LYS cc_start: 0.8958 (tptp) cc_final: 0.8561 (tppt) REVERT: A 924 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7762 (mm-30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1542 time to fit residues: 20.5849 Evaluate side-chains 72 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 HIS A 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.069078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055342 restraints weight = 63501.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058103 restraints weight = 27037.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059836 restraints weight = 15788.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060931 restraints weight = 11148.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.061662 restraints weight = 8866.577| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6260 Z= 0.160 Angle : 0.755 21.142 8559 Z= 0.397 Chirality : 0.042 0.205 987 Planarity : 0.003 0.036 979 Dihedral : 10.372 90.859 1062 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.32), residues: 674 helix: 1.69 (0.28), residues: 326 sheet: -2.86 (0.46), residues: 91 loop : -3.25 (0.33), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1009 TYR 0.012 0.001 TYR A 342 PHE 0.010 0.001 PHE A 401 TRP 0.007 0.001 TRP A 737 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 6256) covalent geometry : angle 0.75298 / 0.40 ( 8553) hydrogen bonds : bond 0.03345 / 2.15 ( 294) hydrogen bonds : angle 4.12425 / 2.84 ( 821) metal coordination : bond 0.00617 / 0.31 ( 4) metal coordination : angle 2.33912 / 0.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 VAL cc_start: 0.9191 (t) cc_final: 0.8964 (p) REVERT: A 580 GLU cc_start: 0.9420 (tt0) cc_final: 0.8790 (tm-30) REVERT: A 586 MET cc_start: 0.9297 (tpp) cc_final: 0.9005 (tpp) REVERT: A 603 GLU cc_start: 0.9092 (tt0) cc_final: 0.8651 (tm-30) REVERT: A 607 LYS cc_start: 0.9601 (mmtt) cc_final: 0.9306 (mmtm) REVERT: A 674 GLU cc_start: 0.8805 (mp0) cc_final: 0.8339 (mp0) REVERT: A 809 LEU cc_start: 0.9203 (tp) cc_final: 0.8788 (tt) REVERT: A 884 LYS cc_start: 0.9085 (tptp) cc_final: 0.8745 (tppt) REVERT: A 924 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 926 MET cc_start: 0.8680 (mtp) cc_final: 0.8434 (ptp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1457 time to fit residues: 18.9106 Evaluate side-chains 73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 0.0040 chunk 66 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN A 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.069051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055242 restraints weight = 63435.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058061 restraints weight = 27067.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059820 restraints weight = 15740.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060940 restraints weight = 11043.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.061585 restraints weight = 8738.568| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6260 Z= 0.103 Angle : 0.713 21.137 8559 Z= 0.374 Chirality : 0.041 0.213 987 Planarity : 0.003 0.042 979 Dihedral : 10.032 86.969 1062 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.31 % Favored : 91.54 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.77 (0.33), residues: 674 helix: 1.95 (0.29), residues: 326 sheet: -2.67 (0.49), residues: 89 loop : -3.10 (0.33), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 606 TYR 0.014 0.001 TYR A 455 PHE 0.008 0.001 PHE A 401 TRP 0.005 0.001 TRP A 968 HIS 0.007 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 6256) covalent geometry : angle 0.71066 / 0.37 ( 8553) hydrogen bonds : bond 0.03081 / 2.01 ( 294) hydrogen bonds : angle 3.85838 / 2.67 ( 821) metal coordination : bond 0.00389 / 0.20 ( 4) metal coordination : angle 2.29286 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8130 (tm-30) REVERT: A 445 GLU cc_start: 0.8496 (mp0) cc_final: 0.8055 (mp0) REVERT: A 454 VAL cc_start: 0.9123 (t) cc_final: 0.8922 (p) REVERT: A 586 MET cc_start: 0.9315 (tpp) cc_final: 0.8937 (tpp) REVERT: A 603 GLU cc_start: 0.9119 (tt0) cc_final: 0.8701 (tm-30) REVERT: A 607 LYS cc_start: 0.9608 (mmtt) cc_final: 0.9293 (mmtm) REVERT: A 739 MET cc_start: 0.8474 (ptt) cc_final: 0.8234 (ppp) REVERT: A 809 LEU cc_start: 0.9215 (tp) cc_final: 0.8775 (tt) REVERT: A 884 LYS cc_start: 0.9181 (tptp) cc_final: 0.8756 (tppt) REVERT: A 924 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7503 (mm-30) REVERT: A 926 MET cc_start: 0.8636 (mtp) cc_final: 0.8397 (ptp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1324 time to fit residues: 18.5695 Evaluate side-chains 79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.0770 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.053763 restraints weight = 66910.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.056495 restraints weight = 28660.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058231 restraints weight = 16678.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059331 restraints weight = 11733.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060060 restraints weight = 9321.137| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6260 Z= 0.171 Angle : 0.763 21.140 8559 Z= 0.398 Chirality : 0.042 0.158 987 Planarity : 0.003 0.037 979 Dihedral : 10.303 84.496 1062 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.39 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.78 (0.33), residues: 674 helix: 1.93 (0.29), residues: 326 sheet: -2.65 (0.50), residues: 90 loop : -3.11 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1009 TYR 0.012 0.001 TYR A 342 PHE 0.013 0.001 PHE A 401 TRP 0.007 0.001 TRP A 737 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 6256) covalent geometry : angle 0.76153 / 0.40 ( 8553) hydrogen bonds : bond 0.03268 / 2.12 ( 294) hydrogen bonds : angle 4.00657 / 2.75 ( 821) metal coordination : bond 0.00707 / 0.36 ( 4) metal coordination : angle 1.98714 / 0.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 444 ASP cc_start: 0.8087 (t70) cc_final: 0.7641 (t70) REVERT: A 445 GLU cc_start: 0.8641 (mp0) cc_final: 0.7667 (mp0) REVERT: A 454 VAL cc_start: 0.9138 (t) cc_final: 0.8873 (p) REVERT: A 505 LYS cc_start: 0.9514 (tmtt) cc_final: 0.9279 (tptt) REVERT: A 586 MET cc_start: 0.9347 (tpp) cc_final: 0.8937 (tpp) REVERT: A 603 GLU cc_start: 0.9214 (tt0) cc_final: 0.8837 (tm-30) REVERT: A 607 LYS cc_start: 0.9623 (mmtt) cc_final: 0.9281 (mmtm) REVERT: A 739 MET cc_start: 0.8402 (ptt) cc_final: 0.8149 (ppp) REVERT: A 809 LEU cc_start: 0.9173 (tp) cc_final: 0.8722 (tt) REVERT: A 884 LYS cc_start: 0.9229 (tptp) cc_final: 0.8819 (tppt) REVERT: A 924 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 926 MET cc_start: 0.8632 (mtp) cc_final: 0.8290 (ptp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1220 time to fit residues: 15.6596 Evaluate side-chains 72 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 21 optimal weight: 0.0470 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 HIS A 759 HIS A 862 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.054984 restraints weight = 64261.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.057754 restraints weight = 27431.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059495 restraints weight = 16001.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060597 restraints weight = 11249.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.061242 restraints weight = 8905.576| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6260 Z= 0.110 Angle : 0.715 21.252 8559 Z= 0.375 Chirality : 0.041 0.192 987 Planarity : 0.003 0.038 979 Dihedral : 9.876 81.287 1062 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.90 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.54 (0.33), residues: 674 helix: 2.14 (0.29), residues: 326 sheet: -2.50 (0.51), residues: 89 loop : -3.01 (0.33), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.014 0.001 TYR A 455 PHE 0.008 0.001 PHE A 401 TRP 0.004 0.001 TRP A 968 HIS 0.007 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 6256) covalent geometry : angle 0.71270 / 0.37 ( 8553) hydrogen bonds : bond 0.02892 / 1.89 ( 294) hydrogen bonds : angle 3.83705 / 2.68 ( 821) metal coordination : bond 0.00440 / 0.22 ( 4) metal coordination : angle 2.05508 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 444 ASP cc_start: 0.8071 (t70) cc_final: 0.7572 (t70) REVERT: A 445 GLU cc_start: 0.8740 (mp0) cc_final: 0.7724 (mp0) REVERT: A 454 VAL cc_start: 0.9154 (t) cc_final: 0.8899 (p) REVERT: A 505 LYS cc_start: 0.9518 (tmtt) cc_final: 0.9296 (tptt) REVERT: A 586 MET cc_start: 0.9348 (tpp) cc_final: 0.8957 (tpp) REVERT: A 603 GLU cc_start: 0.9193 (tt0) cc_final: 0.8803 (tm-30) REVERT: A 607 LYS cc_start: 0.9686 (mmtt) cc_final: 0.9294 (mmtm) REVERT: A 739 MET cc_start: 0.8472 (ptt) cc_final: 0.8248 (ppp) REVERT: A 809 LEU cc_start: 0.9171 (tp) cc_final: 0.8726 (tt) REVERT: A 924 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7059 (mt-10) REVERT: A 926 MET cc_start: 0.8752 (mtp) cc_final: 0.8444 (ptp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1239 time to fit residues: 15.8493 Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.055275 restraints weight = 65523.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058021 restraints weight = 27679.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.059738 restraints weight = 15979.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.060882 restraints weight = 11230.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.061620 restraints weight = 8842.768| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6260 Z= 0.096 Angle : 0.712 21.194 8559 Z= 0.370 Chirality : 0.041 0.192 987 Planarity : 0.003 0.043 979 Dihedral : 9.698 73.856 1062 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.86 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.41 (0.33), residues: 674 helix: 2.16 (0.29), residues: 328 sheet: -2.33 (0.55), residues: 82 loop : -2.90 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.016 0.001 TYR A 455 PHE 0.008 0.001 PHE A 401 TRP 0.003 0.000 TRP A 968 HIS 0.007 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 6256) covalent geometry : angle 0.70339 / 0.37 ( 8553) hydrogen bonds : bond 0.02815 / 1.85 ( 294) hydrogen bonds : angle 3.73839 / 2.62 ( 821) metal coordination : bond 0.00378 / 0.19 ( 4) metal coordination : angle 4.18540 / 1.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 444 ASP cc_start: 0.8058 (t70) cc_final: 0.7544 (t70) REVERT: A 445 GLU cc_start: 0.8697 (mp0) cc_final: 0.7691 (mp0) REVERT: A 505 LYS cc_start: 0.9521 (tmtt) cc_final: 0.9304 (tptt) REVERT: A 586 MET cc_start: 0.9349 (tpp) cc_final: 0.8962 (tpp) REVERT: A 603 GLU cc_start: 0.9208 (tt0) cc_final: 0.8926 (tm-30) REVERT: A 607 LYS cc_start: 0.9692 (mmtt) cc_final: 0.9177 (mmmm) REVERT: A 739 MET cc_start: 0.8458 (ptt) cc_final: 0.8236 (ppp) REVERT: A 809 LEU cc_start: 0.9161 (tp) cc_final: 0.8712 (tt) REVERT: A 924 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 926 MET cc_start: 0.8767 (mtp) cc_final: 0.8428 (ptp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1243 time to fit residues: 16.0678 Evaluate side-chains 74 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 HIS ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.068121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.054785 restraints weight = 65983.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057530 restraints weight = 27371.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059245 restraints weight = 15673.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060363 restraints weight = 10935.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060950 restraints weight = 8601.868| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6260 Z= 0.138 Angle : 0.728 21.194 8559 Z= 0.380 Chirality : 0.040 0.146 987 Planarity : 0.003 0.039 979 Dihedral : 9.857 67.477 1062 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.05 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.46 (0.33), residues: 674 helix: 2.16 (0.29), residues: 327 sheet: -2.43 (0.51), residues: 90 loop : -2.94 (0.33), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.012 0.001 TYR A 455 PHE 0.013 0.001 PHE A 401 TRP 0.004 0.001 TRP A 968 HIS 0.007 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 6256) covalent geometry : angle 0.72659 / 0.38 ( 8553) hydrogen bonds : bond 0.02913 / 1.93 ( 294) hydrogen bonds : angle 3.82803 / 2.68 ( 821) metal coordination : bond 0.00534 / 0.27 ( 4) metal coordination : angle 1.98595 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASP cc_start: 0.8078 (t70) cc_final: 0.7596 (t70) REVERT: A 445 GLU cc_start: 0.8683 (mp0) cc_final: 0.7767 (mp0) REVERT: A 505 LYS cc_start: 0.9515 (tmtt) cc_final: 0.9210 (tptt) REVERT: A 580 GLU cc_start: 0.9378 (tt0) cc_final: 0.8854 (tm-30) REVERT: A 586 MET cc_start: 0.9333 (tpp) cc_final: 0.8962 (tpp) REVERT: A 603 GLU cc_start: 0.9285 (tt0) cc_final: 0.9007 (tm-30) REVERT: A 607 LYS cc_start: 0.9685 (mmtt) cc_final: 0.9174 (mmmm) REVERT: A 674 GLU cc_start: 0.8656 (mp0) cc_final: 0.8195 (mp0) REVERT: A 726 LYS cc_start: 0.9273 (tptp) cc_final: 0.8956 (tptt) REVERT: A 739 MET cc_start: 0.8413 (ptt) cc_final: 0.8164 (ppp) REVERT: A 924 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 926 MET cc_start: 0.8746 (mtp) cc_final: 0.8430 (ptp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1217 time to fit residues: 15.5390 Evaluate side-chains 74 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 HIS A 759 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.068653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055243 restraints weight = 65879.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.057952 restraints weight = 27558.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059654 restraints weight = 15936.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060774 restraints weight = 11198.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.061452 restraints weight = 8854.520| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6260 Z= 0.136 Angle : 0.730 21.219 8559 Z= 0.380 Chirality : 0.041 0.147 987 Planarity : 0.003 0.040 979 Dihedral : 9.792 65.932 1062 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.20 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.40 (0.33), residues: 674 helix: 2.16 (0.29), residues: 329 sheet: -2.17 (0.56), residues: 77 loop : -2.97 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 806 TYR 0.014 0.001 TYR A 455 PHE 0.011 0.001 PHE A 401 TRP 0.004 0.001 TRP A 968 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 6256) covalent geometry : angle 0.72747 / 0.38 ( 8553) hydrogen bonds : bond 0.02782 / 1.84 ( 294) hydrogen bonds : angle 3.78399 / 2.64 ( 821) metal coordination : bond 0.00511 / 0.26 ( 4) metal coordination : angle 2.23386 / 0.83 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 444 ASP cc_start: 0.8103 (t70) cc_final: 0.7559 (t70) REVERT: A 445 GLU cc_start: 0.8642 (mp0) cc_final: 0.7701 (mp0) REVERT: A 505 LYS cc_start: 0.9540 (tmtt) cc_final: 0.9216 (tptt) REVERT: A 580 GLU cc_start: 0.9375 (tt0) cc_final: 0.8859 (tm-30) REVERT: A 586 MET cc_start: 0.9344 (tpp) cc_final: 0.8963 (tpp) REVERT: A 603 GLU cc_start: 0.9283 (tt0) cc_final: 0.9022 (tm-30) REVERT: A 674 GLU cc_start: 0.8644 (mp0) cc_final: 0.8181 (mp0) REVERT: A 739 MET cc_start: 0.8365 (ptt) cc_final: 0.8121 (ppp) REVERT: A 924 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7230 (tp30) REVERT: A 926 MET cc_start: 0.8785 (mtp) cc_final: 0.8400 (ptp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1221 time to fit residues: 14.8904 Evaluate side-chains 71 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 HIS A 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.069079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.055711 restraints weight = 66011.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058539 restraints weight = 27644.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060362 restraints weight = 15737.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.061484 restraints weight = 10871.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.062259 restraints weight = 8497.939| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6260 Z= 0.091 Angle : 0.702 21.253 8559 Z= 0.370 Chirality : 0.041 0.174 987 Planarity : 0.003 0.043 979 Dihedral : 9.469 65.900 1062 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.16 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.24 (0.34), residues: 674 helix: 2.20 (0.29), residues: 330 sheet: -2.01 (0.60), residues: 70 loop : -2.79 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.016 0.001 TYR A 455 PHE 0.007 0.001 PHE A 401 TRP 0.004 0.001 TRP A 968 HIS 0.006 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 6256) covalent geometry : angle 0.70007 / 0.37 ( 8553) hydrogen bonds : bond 0.02714 / 1.75 ( 294) hydrogen bonds : angle 3.69179 / 2.59 ( 821) metal coordination : bond 0.00392 / 0.20 ( 4) metal coordination : angle 2.11440 / 0.71 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.76 seconds wall clock time: 31 minutes 50.02 seconds (1910.02 seconds total)