Starting phenix.real_space_refine on Wed Sep 25 19:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/09_2024/6gjz_0012.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/09_2024/6gjz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/09_2024/6gjz_0012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/09_2024/6gjz_0012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/09_2024/6gjz_0012.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gjz_0012/09_2024/6gjz_0012.cif" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 5.61, per 1000 atoms: 0.53 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: 2.96 Conformation dependent library (CDL) restraints added in 926.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " Number of angles added : 6 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 52.6% alpha, 9.4% beta 14 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 4.58 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: 3.74 Time building geometry restraints manager: 3.50 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: 0.550 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: 0.190 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 32.920 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.300 ------------------------------------------------------------------------------- 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 : 0.011 0.148 6256 Z= 0.760 Angle : 1.109 20.305 8553 Z= 0.619 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.003 TRP A1003 HIS 0.012 0.003 HIS A 506 PHE 0.016 0.002 PHE A 517 TYR 0.024 0.003 TYR A 408 ARG 0.015 0.001 ARG A 619 *********************** 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 fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.969 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: A 444 ASP cc_start: 0.8615 (t70) cc_final: 0.7573 (t70) REVERT: A 520 LYS cc_start: 0.9324 (mmmt) cc_final: 0.9015 (mmmt) REVERT: A 580 GLU cc_start: 0.9384 (tt0) cc_final: 0.9024 (tm-30) REVERT: A 603 GLU cc_start: 0.9287 (tt0) cc_final: 0.8725 (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: 0.9187 (mt) REVERT: A 816 MET cc_start: 0.8771 (ttt) cc_final: 0.8557 (ttt) REVERT: A 884 LYS cc_start: 0.9074 (tptp) cc_final: 0.8631 (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: 0.3817 time to fit residues: 86.4595 Evaluate side-chains 109 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6256 Z= 0.174 Angle : 0.743 21.321 8553 Z= 0.404 Chirality : 0.039 0.156 987 Planarity : 0.004 0.048 979 Dihedral : 16.129 84.706 1200 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.33 % Allowed : 0.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.31), residues: 674 helix: 0.49 (0.28), residues: 324 sheet: -2.95 (0.49), residues: 86 loop : -3.59 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.007 0.001 HIS A 871 PHE 0.007 0.001 PHE A 675 TYR 0.015 0.001 TYR A 455 ARG 0.003 0.000 ARG A 619 *********************** 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 130 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 445 GLU cc_start: 0.8586 (mp0) cc_final: 0.7939 (mp0) REVERT: A 459 MET cc_start: 0.9262 (mmm) cc_final: 0.8941 (mmm) REVERT: A 488 LEU cc_start: 0.9148 (mp) cc_final: 0.8800 (tt) REVERT: A 580 GLU cc_start: 0.9376 (tt0) cc_final: 0.8751 (tm-30) REVERT: A 603 GLU cc_start: 0.9175 (tt0) cc_final: 0.8432 (tm-30) REVERT: A 607 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9193 (mmtm) REVERT: A 790 THR cc_start: 0.8992 (p) cc_final: 0.8555 (p) REVERT: A 884 LYS cc_start: 0.8969 (tptp) cc_final: 0.8541 (tptp) REVERT: A 924 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7991 (mm-30) REVERT: A 931 MET cc_start: 0.7546 (ppp) cc_final: 0.7267 (ppp) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.3435 time to fit residues: 58.4557 Evaluate side-chains 99 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 0.0570 chunk 21 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- 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 531 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6256 Z= 0.212 Angle : 0.728 21.051 8553 Z= 0.399 Chirality : 0.038 0.143 987 Planarity : 0.003 0.042 979 Dihedral : 15.660 89.075 1200 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.79 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.32), residues: 674 helix: 0.97 (0.28), residues: 339 sheet: -2.69 (0.50), residues: 85 loop : -3.40 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.006 0.001 HIS A 927 PHE 0.012 0.001 PHE A 401 TYR 0.015 0.001 TYR A 455 ARG 0.003 0.000 ARG A 619 *********************** 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 107 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.909 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: A 388 ILE cc_start: 0.9038 (tt) cc_final: 0.8796 (mt) REVERT: A 419 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8532 (tp30) REVERT: A 445 GLU cc_start: 0.8501 (mp0) cc_final: 0.8086 (mp0) REVERT: A 459 MET cc_start: 0.9318 (mmm) cc_final: 0.9031 (mmm) REVERT: A 535 GLU cc_start: 0.8384 (mp0) cc_final: 0.7954 (mp0) REVERT: A 580 GLU cc_start: 0.9447 (tt0) cc_final: 0.8900 (tm-30) REVERT: A 586 MET cc_start: 0.9312 (tpp) cc_final: 0.9005 (tpp) REVERT: A 603 GLU cc_start: 0.9136 (tt0) cc_final: 0.8584 (tm-30) REVERT: A 607 LYS cc_start: 0.9568 (mmtt) cc_final: 0.9288 (mmtm) REVERT: A 739 MET cc_start: 0.8604 (ptt) cc_final: 0.8248 (ppp) REVERT: A 884 LYS cc_start: 0.8951 (tptp) cc_final: 0.8751 (tppt) REVERT: A 924 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7866 (mm-30) REVERT: A 931 MET cc_start: 0.7804 (ppp) cc_final: 0.7422 (ppp) REVERT: A 997 LYS cc_start: 0.9327 (mttt) cc_final: 0.9047 (UNCLASSIFIED) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3513 time to fit residues: 49.0856 Evaluate side-chains 79 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 531 HIS A 577 GLN A 759 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6256 Z= 0.325 Angle : 0.776 20.968 8553 Z= 0.429 Chirality : 0.039 0.169 987 Planarity : 0.004 0.034 979 Dihedral : 15.721 102.303 1200 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.28 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.32), residues: 674 helix: 1.27 (0.28), residues: 327 sheet: -2.71 (0.46), residues: 93 loop : -3.47 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 737 HIS 0.008 0.002 HIS A 928 PHE 0.015 0.002 PHE A 401 TYR 0.013 0.002 TYR A 342 ARG 0.005 0.001 ARG A 942 *********************** 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 91 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.964 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: 0.8826 (tm-30) cc_final: 0.8574 (tp30) REVERT: A 454 VAL cc_start: 0.9195 (t) cc_final: 0.8930 (p) REVERT: A 505 LYS cc_start: 0.9501 (tmtt) cc_final: 0.9278 (tptt) REVERT: A 580 GLU cc_start: 0.9508 (tt0) cc_final: 0.8881 (tm-30) REVERT: A 586 MET cc_start: 0.9354 (tpp) cc_final: 0.9134 (tpp) REVERT: A 603 GLU cc_start: 0.9143 (tt0) cc_final: 0.8701 (tm-30) REVERT: A 607 LYS cc_start: 0.9598 (mmtt) cc_final: 0.9306 (mmtm) REVERT: A 884 LYS cc_start: 0.9210 (tptp) cc_final: 0.8770 (tppt) REVERT: A 924 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7606 (mm-30) REVERT: A 931 MET cc_start: 0.8083 (ppp) cc_final: 0.7830 (ppp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3577 time to fit residues: 43.1617 Evaluate side-chains 68 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6256 Z= 0.247 Angle : 0.721 21.063 8553 Z= 0.397 Chirality : 0.038 0.148 987 Planarity : 0.004 0.051 979 Dihedral : 15.527 112.743 1200 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.39 % Favored : 89.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.32), residues: 674 helix: 1.55 (0.28), residues: 325 sheet: -2.81 (0.48), residues: 86 loop : -3.41 (0.31), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 737 HIS 0.009 0.002 HIS A 928 PHE 0.011 0.001 PHE A 401 TYR 0.012 0.001 TYR A 342 ARG 0.008 0.001 ARG A 310 *********************** 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 88 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.878 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: A 419 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8562 (tp30) REVERT: A 505 LYS cc_start: 0.9508 (tmtt) cc_final: 0.9186 (tptt) REVERT: A 580 GLU cc_start: 0.9474 (tt0) cc_final: 0.9243 (tt0) REVERT: A 586 MET cc_start: 0.9349 (tpp) cc_final: 0.9041 (tpp) REVERT: A 603 GLU cc_start: 0.9173 (tt0) cc_final: 0.8803 (tm-30) REVERT: A 607 LYS cc_start: 0.9622 (mmtt) cc_final: 0.9290 (mmtm) REVERT: A 739 MET cc_start: 0.8439 (ptt) cc_final: 0.8134 (ppp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3323 time to fit residues: 39.7252 Evaluate side-chains 71 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 0.0060 chunk 35 optimal weight: 9.9990 chunk 65 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 2.4202 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6256 Z= 0.190 Angle : 0.693 21.073 8553 Z= 0.381 Chirality : 0.037 0.143 987 Planarity : 0.003 0.049 979 Dihedral : 15.457 113.198 1200 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.53 % Favored : 89.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.33), residues: 674 helix: 1.86 (0.28), residues: 325 sheet: -2.75 (0.51), residues: 89 loop : -3.16 (0.32), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 968 HIS 0.007 0.001 HIS A 928 PHE 0.011 0.001 PHE A 401 TYR 0.012 0.001 TYR A 342 ARG 0.003 0.000 ARG A 310 *********************** 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 87 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.991 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: 0.8893 (tm-30) cc_final: 0.8610 (tp30) REVERT: A 445 GLU cc_start: 0.8692 (mp0) cc_final: 0.8005 (mp0) REVERT: A 505 LYS cc_start: 0.9514 (tmtt) cc_final: 0.9180 (tptt) REVERT: A 580 GLU cc_start: 0.9467 (tt0) cc_final: 0.8901 (tm-30) REVERT: A 586 MET cc_start: 0.9365 (tpp) cc_final: 0.9031 (tpp) REVERT: A 603 GLU cc_start: 0.9182 (tt0) cc_final: 0.8906 (tm-30) REVERT: A 607 LYS cc_start: 0.9703 (mmtt) cc_final: 0.9230 (mmmm) REVERT: A 674 GLU cc_start: 0.9053 (mp0) cc_final: 0.8819 (mm-30) REVERT: A 739 MET cc_start: 0.8380 (ptt) cc_final: 0.8106 (ppp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2964 time to fit residues: 35.5292 Evaluate side-chains 72 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 31 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 A 862 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6256 Z= 0.130 Angle : 0.669 21.249 8553 Z= 0.365 Chirality : 0.037 0.141 987 Planarity : 0.003 0.043 979 Dihedral : 15.356 110.703 1200 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.34), residues: 674 helix: 2.16 (0.29), residues: 326 sheet: -2.58 (0.52), residues: 89 loop : -3.04 (0.33), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 582 HIS 0.005 0.001 HIS A 531 PHE 0.007 0.001 PHE A 551 TYR 0.015 0.001 TYR A 455 ARG 0.003 0.000 ARG A 606 *********************** 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 94 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8609 (tp30) REVERT: A 445 GLU cc_start: 0.8639 (mp0) cc_final: 0.7916 (mp0) REVERT: A 505 LYS cc_start: 0.9505 (tmtt) cc_final: 0.9171 (tptt) REVERT: A 580 GLU cc_start: 0.9451 (tt0) cc_final: 0.9233 (tt0) REVERT: A 586 MET cc_start: 0.9368 (tpp) cc_final: 0.9024 (tpp) REVERT: A 603 GLU cc_start: 0.9207 (tt0) cc_final: 0.8921 (tm-30) REVERT: A 607 LYS cc_start: 0.9690 (mmtt) cc_final: 0.9182 (mmmm) REVERT: A 674 GLU cc_start: 0.9054 (mp0) cc_final: 0.8758 (mm-30) REVERT: A 739 MET cc_start: 0.8391 (ptt) cc_final: 0.8093 (ppp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.3032 time to fit residues: 38.8610 Evaluate side-chains 74 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6256 Z= 0.213 Angle : 0.708 21.128 8553 Z= 0.387 Chirality : 0.037 0.141 987 Planarity : 0.003 0.043 979 Dihedral : 15.461 111.385 1200 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.39 % Favored : 89.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.33), residues: 674 helix: 2.14 (0.29), residues: 325 sheet: -2.56 (0.49), residues: 97 loop : -3.18 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 968 HIS 0.007 0.001 HIS A 871 PHE 0.013 0.001 PHE A 401 TYR 0.014 0.001 TYR A 455 ARG 0.023 0.001 ARG A 547 *********************** 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 86 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.845 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: A 419 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8633 (tp30) REVERT: A 505 LYS cc_start: 0.9530 (tmtt) cc_final: 0.9195 (tptt) REVERT: A 586 MET cc_start: 0.9367 (tpp) cc_final: 0.9028 (tpp) REVERT: A 603 GLU cc_start: 0.9228 (tt0) cc_final: 0.8979 (tm-30) REVERT: A 739 MET cc_start: 0.8451 (ptt) cc_final: 0.8147 (ppp) REVERT: A 926 MET cc_start: 0.8472 (ptt) cc_final: 0.8251 (ptt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3223 time to fit residues: 38.1906 Evaluate side-chains 70 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 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 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6256 Z= 0.233 Angle : 0.715 21.208 8553 Z= 0.392 Chirality : 0.038 0.149 987 Planarity : 0.003 0.042 979 Dihedral : 15.511 118.607 1200 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.68 % Favored : 89.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.33), residues: 674 helix: 2.02 (0.29), residues: 325 sheet: -2.51 (0.50), residues: 96 loop : -3.20 (0.32), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 737 HIS 0.009 0.002 HIS A 928 PHE 0.016 0.001 PHE A 401 TYR 0.013 0.002 TYR A 455 ARG 0.003 0.000 ARG A 860 *********************** 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 84 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.917 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: A 419 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8640 (tp30) REVERT: A 505 LYS cc_start: 0.9532 (tmtt) cc_final: 0.9181 (tptt) REVERT: A 580 GLU cc_start: 0.9458 (tt0) cc_final: 0.8914 (tm-30) REVERT: A 586 MET cc_start: 0.9374 (tpp) cc_final: 0.9041 (tpp) REVERT: A 603 GLU cc_start: 0.9227 (tt0) cc_final: 0.8989 (tm-30) REVERT: A 926 MET cc_start: 0.8728 (ptt) cc_final: 0.8470 (ptt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3074 time to fit residues: 35.4167 Evaluate side-chains 68 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6256 Z= 0.157 Angle : 0.690 21.232 8553 Z= 0.375 Chirality : 0.037 0.142 987 Planarity : 0.003 0.045 979 Dihedral : 15.459 121.791 1200 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.09 % Favored : 89.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.33), residues: 674 helix: 2.15 (0.29), residues: 326 sheet: -2.40 (0.51), residues: 96 loop : -3.08 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 968 HIS 0.007 0.001 HIS A 928 PHE 0.009 0.001 PHE A 401 TYR 0.011 0.001 TYR A 455 ARG 0.003 0.000 ARG A 547 ********************** 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 87 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.859 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: A 419 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8604 (tp30) REVERT: A 445 GLU cc_start: 0.8686 (mp0) cc_final: 0.8055 (mp0) REVERT: A 505 LYS cc_start: 0.9545 (tmtt) cc_final: 0.9211 (tptt) REVERT: A 580 GLU cc_start: 0.9455 (tt0) cc_final: 0.8916 (tm-30) REVERT: A 586 MET cc_start: 0.9373 (tpp) cc_final: 0.9033 (tpp) REVERT: A 603 GLU cc_start: 0.9292 (tt0) cc_final: 0.9043 (tm-30) REVERT: A 739 MET cc_start: 0.8427 (ptt) cc_final: 0.8187 (ppp) REVERT: A 931 MET cc_start: 0.8430 (ppp) cc_final: 0.8224 (ppp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2977 time to fit residues: 35.5809 Evaluate side-chains 69 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3308 r_free = 0.3308 target = 0.065846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052899 restraints weight = 67438.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055538 restraints weight = 28126.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057213 restraints weight = 16131.360| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6256 Z= 0.293 Angle : 0.746 21.050 8553 Z= 0.409 Chirality : 0.038 0.145 987 Planarity : 0.003 0.042 979 Dihedral : 15.823 129.148 1200 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.13 % Favored : 88.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.33), residues: 674 helix: 1.68 (0.28), residues: 329 sheet: -2.58 (0.49), residues: 98 loop : -3.19 (0.33), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1003 HIS 0.010 0.002 HIS A 928 PHE 0.018 0.001 PHE A 401 TYR 0.016 0.002 TYR A 455 ARG 0.003 0.000 ARG A 860 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.35 seconds wall clock time: 45 minutes 44.18 seconds (2744.18 seconds total)