Starting phenix.real_space_refine on Wed Sep 17 20:11:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gjz_0012/09_2025/6gjz_0012.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gjz_0012/09_2025/6gjz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2025/6gjz_0012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2025/6gjz_0012.map" model { file = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2025/6gjz_0012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gjz_0012/09_2025/6gjz_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 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: {'RNA': 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: 2.25, per 1000 atoms: 0.21 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: 1.11 Conformation dependent library (CDL) restraints added in 236.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.26 Time building geometry restraints manager: 1.47 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: 5052 17.46 - 34.91: 213 34.91 - 52.37: 58 52.37 - 69.83: 42 69.83 - 87.28: 24 Dihedral angle restraints: 5389 sinusoidal: 3123 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 5386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 716 0.053 - 0.107: 224 0.107 - 0.160: 40 0.160 - 0.213: 5 0.213 - 0.266: 2 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=" CB VAL A 316 " pdb=" CA VAL A 316 " pdb=" CG1 VAL A 316 " pdb=" CG2 VAL A 316 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.53e-01 ... (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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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= 0.639 Angle : 1.170 25.798 8559 Z= 0.622 Chirality : 0.052 0.266 987 Planarity : 0.006 0.049 979 Dihedral : 14.450 87.282 2625 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 aren 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 covalent geometry : bond 0.01150 ( 6256) covalent geometry : angle 1.10920 ( 8553) hydrogen bonds : bond 0.13733 ( 294) hydrogen bonds : angle 6.67237 ( 821) metal coordination : bond 0.30719 ( 4) metal coordination : angle 14.05327 ( 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 : 0.323 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: 0.8611 (mm-30) cc_final: 0.8117 (mt-10) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1777 time to fit residues: 40.3350 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 : 0.301 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3456 r_free = 0.3456 target = 0.071668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057909 restraints weight = 62045.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060975 restraints weight = 25845.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062885 restraints weight = 14595.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.064108 restraints weight = 9988.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.064860 restraints weight = 7725.336| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6260 Z= 0.136 Angle : 0.747 21.294 8559 Z= 0.405 Chirality : 0.039 0.152 987 Planarity : 0.004 0.048 979 Dihedral : 16.163 84.720 1200 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % 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 aren not related in a simple way. whole: -2.27 (0.31), residues: 674 helix: 0.48 (0.28), residues: 322 sheet: -2.96 (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 0.015 0.001 TYR A 455 PHE 0.007 0.001 PHE A 849 TRP 0.007 0.001 TRP A 737 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6256) covalent geometry : angle 0.74165 ( 8553) hydrogen bonds : bond 0.04284 ( 294) hydrogen bonds : angle 4.63537 ( 821) metal coordination : bond 0.01672 ( 4) metal coordination : angle 3.30297 ( 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 129 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.347 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: symmetry clash REVERT: A 445 GLU cc_start: 0.8616 (mp0) cc_final: 0.7942 (mp0) REVERT: A 459 MET cc_start: 0.9328 (mmm) cc_final: 0.9036 (mmm) REVERT: A 488 LEU cc_start: 0.9127 (mp) cc_final: 0.8801 (tt) REVERT: A 580 GLU cc_start: 0.9369 (tt0) cc_final: 0.8750 (tm-30) REVERT: A 603 GLU cc_start: 0.9190 (tt0) cc_final: 0.8418 (tm-30) REVERT: A 607 LYS cc_start: 0.9505 (mmtt) cc_final: 0.9208 (mmtm) REVERT: A 790 THR cc_start: 0.9038 (p) cc_final: 0.8581 (p) REVERT: A 884 LYS cc_start: 0.8983 (tptp) cc_final: 0.8500 (tppt) REVERT: A 924 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 926 MET cc_start: 0.8540 (mtp) cc_final: 0.8234 (ptp) REVERT: A 931 MET cc_start: 0.7424 (ppp) cc_final: 0.7146 (ppp) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.1580 time to fit residues: 26.7229 Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 5.9990 chunk 49 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A 577 GLN 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 = 0.3382 r_free = 0.3382 target = 0.068374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.054695 restraints weight = 66035.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.057515 restraints weight = 28001.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059295 restraints weight = 16294.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060333 restraints weight = 11474.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061144 restraints weight = 9221.601| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6260 Z= 0.214 Angle : 0.775 21.105 8559 Z= 0.422 Chirality : 0.038 0.144 987 Planarity : 0.004 0.038 979 Dihedral : 15.734 92.833 1200 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.94 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 aren not related in a simple way. whole: -1.63 (0.32), residues: 674 helix: 0.97 (0.28), residues: 333 sheet: -2.70 (0.49), residues: 86 loop : -3.40 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 619 TYR 0.014 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 covalent geometry : bond 0.00424 ( 6256) covalent geometry : angle 0.77243 ( 8553) hydrogen bonds : bond 0.03975 ( 294) hydrogen bonds : angle 4.48373 ( 821) metal coordination : bond 0.00648 ( 4) metal coordination : angle 2.67604 ( 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 99 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.287 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: 0.9047 (tt) cc_final: 0.8811 (mt) REVERT: A 445 GLU cc_start: 0.8538 (mp0) cc_final: 0.8284 (mp0) REVERT: A 459 MET cc_start: 0.9314 (mmm) cc_final: 0.9024 (mmm) REVERT: A 488 LEU cc_start: 0.8891 (mp) cc_final: 0.8650 (tt) REVERT: A 535 GLU cc_start: 0.8270 (mp0) cc_final: 0.7855 (mp0) REVERT: A 580 GLU cc_start: 0.9452 (tt0) cc_final: 0.8904 (tm-30) REVERT: A 586 MET cc_start: 0.9310 (tpp) cc_final: 0.9006 (tpp) REVERT: A 603 GLU cc_start: 0.9138 (tt0) cc_final: 0.8624 (tm-30) REVERT: A 607 LYS cc_start: 0.9584 (mmtt) cc_final: 0.9333 (mmtm) REVERT: A 739 MET cc_start: 0.8533 (ptt) cc_final: 0.8193 (ppp) REVERT: A 884 LYS cc_start: 0.8990 (tptp) cc_final: 0.8778 (tppt) REVERT: A 924 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7709 (mm-30) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1728 time to fit residues: 22.1415 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 : 0.290 ------------------------------------------------------------------------------- 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: 0.9980 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: 5.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 531 HIS ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.067452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054029 restraints weight = 65313.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056764 restraints weight = 27404.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058504 restraints weight = 15840.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.059590 restraints weight = 11172.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060222 restraints weight = 8820.812| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6260 Z= 0.213 Angle : 0.762 21.164 8559 Z= 0.417 Chirality : 0.039 0.170 987 Planarity : 0.003 0.034 979 Dihedral : 15.670 100.513 1200 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.39 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % 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 aren not related in a simple way. whole: -1.42 (0.31), residues: 674 helix: 1.37 (0.28), residues: 326 sheet: -3.03 (0.45), residues: 92 loop : -3.34 (0.32), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 824 TYR 0.013 0.001 TYR A 342 PHE 0.015 0.001 PHE A 675 TRP 0.010 0.001 TRP A 737 HIS 0.009 0.002 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 6256) covalent geometry : angle 0.75961 ( 8553) hydrogen bonds : bond 0.03688 ( 294) hydrogen bonds : angle 4.34310 ( 821) metal coordination : bond 0.00849 ( 4) metal coordination : angle 2.17539 ( 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 94 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.308 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 445 GLU cc_start: 0.8581 (mp0) cc_final: 0.8052 (mp0) REVERT: A 454 VAL cc_start: 0.9275 (t) cc_final: 0.9022 (p) REVERT: A 505 LYS cc_start: 0.9506 (tmtt) cc_final: 0.9191 (tptt) REVERT: A 580 GLU cc_start: 0.9476 (tt0) cc_final: 0.8976 (tm-30) REVERT: A 603 GLU cc_start: 0.9095 (tt0) cc_final: 0.8682 (tm-30) REVERT: A 607 LYS cc_start: 0.9626 (mmtt) cc_final: 0.9336 (mmtm) REVERT: A 674 GLU cc_start: 0.8958 (mp0) cc_final: 0.8508 (mp0) REVERT: A 884 LYS cc_start: 0.9268 (tptp) cc_final: 0.8848 (tppt) REVERT: A 924 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 926 MET cc_start: 0.8778 (mtp) cc_final: 0.8440 (ptp) REVERT: A 997 LYS cc_start: 0.9318 (mttt) cc_final: 0.9106 (mtmt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1722 time to fit residues: 21.0349 Evaluate side-chains 70 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 4.9990 chunk 61 optimal weight: 0.0010 chunk 66 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 52 optimal weight: 0.4980 chunk 1 optimal weight: 0.0980 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3373 r_free = 0.3373 target = 0.068728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055226 restraints weight = 64444.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058044 restraints weight = 27126.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059837 restraints weight = 15610.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060882 restraints weight = 10846.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061648 restraints weight = 8654.530| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6260 Z= 0.105 Angle : 0.686 21.235 8559 Z= 0.373 Chirality : 0.037 0.144 987 Planarity : 0.003 0.040 979 Dihedral : 15.529 97.880 1200 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.61 % Favored : 91.25 % 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 aren not related in a simple way. whole: -0.82 (0.33), residues: 674 helix: 1.92 (0.29), residues: 326 sheet: -2.66 (0.49), residues: 89 loop : -3.16 (0.33), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1009 TYR 0.013 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 928 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6256) covalent geometry : angle 0.68357 ( 8553) hydrogen bonds : bond 0.03051 ( 294) hydrogen bonds : angle 3.93925 ( 821) metal coordination : bond 0.00450 ( 4) metal coordination : angle 2.25064 ( 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 94 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.293 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 419 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 445 GLU cc_start: 0.8652 (mp0) cc_final: 0.7929 (mp0) REVERT: A 454 VAL cc_start: 0.9215 (t) cc_final: 0.8964 (p) REVERT: A 505 LYS cc_start: 0.9503 (tmtt) cc_final: 0.9279 (tptt) REVERT: A 580 GLU cc_start: 0.9479 (tt0) cc_final: 0.8962 (tm-30) REVERT: A 586 MET cc_start: 0.9372 (tpp) cc_final: 0.9003 (tpp) REVERT: A 603 GLU cc_start: 0.9111 (tt0) cc_final: 0.8800 (tm-30) REVERT: A 607 LYS cc_start: 0.9619 (mmtt) cc_final: 0.9354 (mmtm) REVERT: A 739 MET cc_start: 0.8492 (ptt) cc_final: 0.8257 (ppp) REVERT: A 884 LYS cc_start: 0.9246 (tptp) cc_final: 0.8844 (tppt) REVERT: A 912 MET cc_start: 0.8278 (ptt) cc_final: 0.7705 (ppp) REVERT: A 924 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 926 MET cc_start: 0.8740 (mtp) cc_final: 0.8356 (ptp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1591 time to fit residues: 19.7794 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 : 0.394 ------------------------------------------------------------------------------- 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: 9.9990 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 0.0070 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 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 = 0.3379 r_free = 0.3379 target = 0.068657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055265 restraints weight = 66219.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058091 restraints weight = 27974.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059871 restraints weight = 16139.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.060915 restraints weight = 11181.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061697 restraints weight = 8876.275| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5703 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= 0.109 Angle : 0.681 21.181 8559 Z= 0.372 Chirality : 0.037 0.145 987 Planarity : 0.003 0.045 979 Dihedral : 15.438 93.945 1200 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.50 % Favored : 90.36 % 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 aren not related in a simple way. whole: -0.66 (0.33), residues: 674 helix: 2.01 (0.29), residues: 326 sheet: -2.40 (0.52), residues: 89 loop : -3.10 (0.33), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.012 0.001 TYR A 455 PHE 0.009 0.001 PHE A 401 TRP 0.004 0.001 TRP A 968 HIS 0.005 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6256) covalent geometry : angle 0.67873 ( 8553) hydrogen bonds : bond 0.02974 ( 294) hydrogen bonds : angle 3.85372 ( 821) metal coordination : bond 0.00484 ( 4) metal coordination : angle 2.20567 ( 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 92 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.281 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 445 GLU cc_start: 0.8655 (mp0) cc_final: 0.7971 (mp0) REVERT: A 454 VAL cc_start: 0.9167 (t) cc_final: 0.8910 (p) REVERT: A 505 LYS cc_start: 0.9511 (tmtt) cc_final: 0.9260 (tptt) REVERT: A 580 GLU cc_start: 0.9496 (tt0) cc_final: 0.8964 (tm-30) REVERT: A 586 MET cc_start: 0.9389 (tpp) cc_final: 0.9012 (tpp) REVERT: A 603 GLU cc_start: 0.9168 (tt0) cc_final: 0.8916 (tm-30) REVERT: A 607 LYS cc_start: 0.9637 (mmtt) cc_final: 0.9350 (mmtm) REVERT: A 739 MET cc_start: 0.8441 (ptt) cc_final: 0.8195 (ppp) REVERT: A 924 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7196 (mm-30) REVERT: A 926 MET cc_start: 0.8745 (mtp) cc_final: 0.8332 (ptp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1528 time to fit residues: 18.8519 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 : 0.363 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3346 r_free = 0.3346 target = 0.067535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054079 restraints weight = 66442.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056812 restraints weight = 28178.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058526 restraints weight = 16448.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.059657 restraints weight = 11622.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060324 restraints weight = 9148.200| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6260 Z= 0.183 Angle : 0.712 21.156 8559 Z= 0.390 Chirality : 0.037 0.142 987 Planarity : 0.003 0.039 979 Dihedral : 15.539 96.121 1200 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.39 % Favored : 89.47 % 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 aren not related in a simple way. whole: -0.76 (0.33), residues: 674 helix: 1.98 (0.29), residues: 326 sheet: -2.47 (0.50), residues: 97 loop : -3.20 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 843 TYR 0.011 0.001 TYR A 455 PHE 0.014 0.001 PHE A 401 TRP 0.005 0.001 TRP A 737 HIS 0.009 0.002 HIS A 871 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6256) covalent geometry : angle 0.71002 ( 8553) hydrogen bonds : bond 0.03196 ( 294) hydrogen bonds : angle 4.09017 ( 821) metal coordination : bond 0.00748 ( 4) metal coordination : angle 1.93854 ( 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 90 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.302 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 505 LYS cc_start: 0.9531 (tmtt) cc_final: 0.9201 (tptt) REVERT: A 580 GLU cc_start: 0.9489 (tt0) cc_final: 0.9007 (tm-30) REVERT: A 586 MET cc_start: 0.9379 (tpp) cc_final: 0.9002 (tpp) REVERT: A 674 GLU cc_start: 0.8608 (mp0) cc_final: 0.8226 (mp0) REVERT: A 924 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7301 (tp30) REVERT: A 926 MET cc_start: 0.8640 (mtp) cc_final: 0.8211 (ptp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1561 time to fit residues: 18.9304 Evaluate side-chains 68 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3364 r_free = 0.3364 target = 0.068383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055574 restraints weight = 65665.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058276 restraints weight = 27646.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.059996 restraints weight = 15900.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061015 restraints weight = 10982.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061790 restraints weight = 8699.739| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6260 Z= 0.107 Angle : 0.680 21.303 8559 Z= 0.370 Chirality : 0.037 0.141 987 Planarity : 0.003 0.042 979 Dihedral : 15.326 96.808 1200 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % 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 aren not related in a simple way. whole: -0.46 (0.34), residues: 674 helix: 2.22 (0.29), residues: 326 sheet: -2.39 (0.53), residues: 89 loop : -3.02 (0.33), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.016 0.001 TYR A 455 PHE 0.010 0.001 PHE A 401 TRP 0.004 0.001 TRP A 582 HIS 0.007 0.001 HIS A 871 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6256) covalent geometry : angle 0.67844 ( 8553) hydrogen bonds : bond 0.02831 ( 294) hydrogen bonds : angle 3.83597 ( 821) metal coordination : bond 0.00520 ( 4) metal coordination : angle 1.80777 ( 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 89 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.301 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 444 ASP cc_start: 0.8140 (t70) cc_final: 0.7545 (t70) REVERT: A 445 GLU cc_start: 0.8664 (mp0) cc_final: 0.7652 (mp0) REVERT: A 505 LYS cc_start: 0.9531 (tmtt) cc_final: 0.9210 (tptt) REVERT: A 580 GLU cc_start: 0.9467 (tt0) cc_final: 0.8969 (tm-30) REVERT: A 586 MET cc_start: 0.9380 (tpp) cc_final: 0.8979 (tpp) REVERT: A 674 GLU cc_start: 0.8659 (mp0) cc_final: 0.8237 (mp0) REVERT: A 924 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 926 MET cc_start: 0.8716 (mtp) cc_final: 0.8327 (ptp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1427 time to fit residues: 17.2836 Evaluate side-chains 67 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.054753 restraints weight = 67027.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057461 restraints weight = 28452.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059183 restraints weight = 16461.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060299 restraints weight = 11461.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060931 restraints weight = 8953.044| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6443 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= 0.128 Angle : 0.686 21.213 8559 Z= 0.373 Chirality : 0.037 0.140 987 Planarity : 0.003 0.041 979 Dihedral : 15.397 96.418 1200 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.79 % Favored : 90.06 % 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 aren not related in a simple way. whole: -0.50 (0.33), residues: 674 helix: 2.18 (0.29), residues: 327 sheet: -2.33 (0.51), residues: 96 loop : -3.09 (0.33), residues: 251 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 0.011 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 covalent geometry : bond 0.00263 ( 6256) covalent geometry : angle 0.68497 ( 8553) hydrogen bonds : bond 0.02855 ( 294) hydrogen bonds : angle 3.83756 ( 821) metal coordination : bond 0.00595 ( 4) metal coordination : angle 1.61403 ( 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 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.205 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: A 394 ASP cc_start: 0.8984 (t0) cc_final: 0.8735 (t0) REVERT: A 444 ASP cc_start: 0.8112 (t70) cc_final: 0.7577 (t70) REVERT: A 505 LYS cc_start: 0.9523 (tmtt) cc_final: 0.9173 (tptt) REVERT: A 580 GLU cc_start: 0.9459 (tt0) cc_final: 0.8980 (tm-30) REVERT: A 586 MET cc_start: 0.9375 (tpp) cc_final: 0.8981 (tpp) REVERT: A 674 GLU cc_start: 0.8637 (mp0) cc_final: 0.8213 (mp0) REVERT: A 797 ASP cc_start: 0.8834 (p0) cc_final: 0.8622 (p0) REVERT: A 924 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7144 (tp30) REVERT: A 926 MET cc_start: 0.8737 (mtp) cc_final: 0.8334 (ptp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1441 time to fit residues: 16.8054 Evaluate side-chains 68 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.068756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055658 restraints weight = 65991.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058418 restraints weight = 28142.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060192 restraints weight = 16309.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061330 restraints weight = 11316.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062008 restraints weight = 8832.542| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6260 Z= 0.091 Angle : 0.677 21.296 8559 Z= 0.368 Chirality : 0.037 0.140 987 Planarity : 0.003 0.043 979 Dihedral : 15.293 95.695 1200 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.64 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 aren not related in a simple way. whole: -0.30 (0.34), residues: 674 helix: 2.31 (0.29), residues: 326 sheet: -2.32 (0.53), residues: 89 loop : -2.88 (0.34), residues: 259 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 0.005 0.001 TRP A 582 HIS 0.006 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 6256) covalent geometry : angle 0.67556 ( 8553) hydrogen bonds : bond 0.02741 ( 294) hydrogen bonds : angle 3.74944 ( 821) metal coordination : bond 0.00415 ( 4) metal coordination : angle 1.69615 ( 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 86 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.302 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 444 ASP cc_start: 0.8192 (t70) cc_final: 0.7714 (t70) REVERT: A 505 LYS cc_start: 0.9536 (tmtt) cc_final: 0.9209 (tptt) REVERT: A 580 GLU cc_start: 0.9469 (tt0) cc_final: 0.8975 (tm-30) REVERT: A 586 MET cc_start: 0.9389 (tpp) cc_final: 0.8983 (tpp) REVERT: A 674 GLU cc_start: 0.8663 (mp0) cc_final: 0.8203 (mp0) REVERT: A 853 MET cc_start: 0.8855 (ttm) cc_final: 0.8644 (ttp) REVERT: A 924 GLU cc_start: 0.7726 (mm-30) cc_final: 0.6954 (tp30) REVERT: A 926 MET cc_start: 0.8811 (mtp) cc_final: 0.8366 (ptp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1474 time to fit residues: 17.2602 Evaluate side-chains 69 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.068470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055430 restraints weight = 67281.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.058199 restraints weight = 28172.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059986 restraints weight = 16216.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061122 restraints weight = 11226.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061877 restraints weight = 8730.547| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6260 Z= 0.100 Angle : 0.676 21.231 8559 Z= 0.367 Chirality : 0.037 0.137 987 Planarity : 0.003 0.042 979 Dihedral : 15.309 92.860 1200 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.61 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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 aren not related in a simple way. whole: -0.37 (0.34), residues: 674 helix: 2.15 (0.29), residues: 329 sheet: -2.18 (0.52), residues: 96 loop : -2.90 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.016 0.001 TYR A 455 PHE 0.009 0.001 PHE A 401 TRP 0.004 0.001 TRP A 968 HIS 0.006 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 6256) covalent geometry : angle 0.67449 ( 8553) hydrogen bonds : bond 0.02735 ( 294) hydrogen bonds : angle 3.75767 ( 821) metal coordination : bond 0.00430 ( 4) metal coordination : angle 1.63641 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.28 seconds wall clock time: 32 minutes 56.79 seconds (1976.79 seconds total)