Starting phenix.real_space_refine on Mon Jun 9 23:26:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gkh_0023/06_2025/6gkh_0023_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gkh_0023/06_2025/6gkh_0023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gkh_0023/06_2025/6gkh_0023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gkh_0023/06_2025/6gkh_0023.map" model { file = "/net/cci-nas-00/data/ceres_data/6gkh_0023/06_2025/6gkh_0023_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gkh_0023/06_2025/6gkh_0023_trim.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= 0.011 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: 10 Type Number sf(0) Gaussians Zn 1 6.06 5 Al 1 5.89 5 P 32 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 3789 2.51 5 N 1075 2.21 5 O 1250 1.98 5 F 4 1.80 5 H 4399 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10587 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 9914 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 21, 'TRANS': 663} Chain breaks: 2 Chain: "X" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 328 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 4} Link IDs: {'rna3p': 14} Chain: "Y" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 311 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8417 SG CYS A 907 77.074 41.795 44.018 1.00119.62 S ATOM 8464 SG CYS A 910 80.344 42.268 44.261 1.00121.44 S ATOM 9081 SG CYS A 962 78.439 43.268 47.617 1.00122.38 S ATOM 9100 SG CYS A 964 78.709 44.849 45.264 1.00121.08 S Time building chain proxies: 6.32, per 1000 atoms: 0.60 Number of scatterers: 10587 At special positions: 0 Unit cell: (98.44, 89.88, 80.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 1 29.99 S 35 16.00 P 32 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1250 8.00 N 1075 7.00 C 3789 6.00 H 4399 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: 3.10 Conformation dependent library (CDL) restraints added in 989.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1104 " pdb="ZN ZN A1104 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1104 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1104 " - pdb=" SG CYS A 907 " pdb="ZN ZN A1104 " - pdb=" SG CYS A 964 " Number of angles added : 6 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1310 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 51.4% alpha, 9.8% beta 14 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 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 376 removed outlier: 4.576A pdb=" N GLU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 400 through 406 removed outlier: 3.685A pdb=" N VAL A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.781A 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 453 through 474 removed outlier: 3.816A pdb=" N ASN A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 474 " --> pdb=" O ASN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.687A pdb=" N ALA A 503 " --> pdb=" O LYS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.753A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.605A pdb=" N ILE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.703A pdb=" N GLU A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.848A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 692 removed outlier: 4.176A pdb=" N ASP A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 716 removed outlier: 4.040A pdb=" N GLU A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 741 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.955A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 780 Processing helix chain 'A' and resid 789 through 793 removed outlier: 3.958A pdb=" N GLU A 793 " --> pdb=" O THR A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 removed outlier: 3.660A pdb=" N MET A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 863 removed outlier: 3.871A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 890 Processing helix chain 'A' and resid 932 through 937 Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.504A pdb=" N ILE A 326 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N THR A 489 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 328 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER A 413 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 362 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 540 through 543 removed outlier: 6.215A pdb=" N VAL A 541 " --> pdb=" O THR A 834 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 751 through 752 removed outlier: 6.571A pdb=" N HIS A 752 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 915 removed outlier: 6.353A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (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: 4.029A pdb=" N GLU A 959 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 969 " --> pdb=" O ILE A 960 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4388 1.03 - 1.22: 18 1.22 - 1.42: 2630 1.42 - 1.62: 3652 1.62 - 1.81: 60 Bond restraints: 10748 Sorted by residual: bond pdb=" F1 ALF A1102 " pdb="AL ALF A1102 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" F3 ALF A1102 " pdb="AL ALF A1102 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" F4 ALF A1102 " pdb="AL ALF A1102 " ideal model delta sigma weight residual 1.686 1.784 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" F2 ALF A1102 " pdb="AL ALF A1102 " ideal model delta sigma weight residual 1.685 1.780 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" CB LYS A 336 " pdb=" CG LYS A 336 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.85e+00 ... (remaining 10743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.24: 18723 14.24 - 28.48: 8 28.48 - 42.72: 0 42.72 - 56.96: 16 56.96 - 71.20: 2 Bond angle restraints: 18749 Sorted by residual: angle pdb=" F1 ALF A1102 " pdb="AL ALF A1102 " pdb=" F2 ALF A1102 " ideal model delta sigma weight residual 108.68 179.88 -71.20 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F3 ALF A1102 " pdb="AL ALF A1102 " pdb=" F4 ALF A1102 " ideal model delta sigma weight residual 109.63 179.30 -69.67 3.00e+00 1.11e-01 5.39e+02 angle pdb=" C LYS A 884 " pdb=" N LYS A 885 " pdb=" H LYS A 885 " ideal model delta sigma weight residual 124.88 70.69 54.19 3.00e+00 1.11e-01 3.26e+02 angle pdb=" C GLU A 793 " pdb=" N GLU A 794 " pdb=" H GLU A 794 " ideal model delta sigma weight residual 123.79 69.60 54.19 3.00e+00 1.11e-01 3.26e+02 angle pdb=" C MET A 886 " pdb=" N LYS A 887 " pdb=" H LYS A 887 " ideal model delta sigma weight residual 125.01 70.84 54.17 3.00e+00 1.11e-01 3.26e+02 ... (remaining 18744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 5062 15.28 - 30.56: 208 30.56 - 45.84: 75 45.84 - 61.13: 50 61.13 - 76.41: 31 Dihedral angle restraints: 5426 sinusoidal: 3149 harmonic: 2277 Sorted by residual: dihedral pdb=" CA SER A 413 " pdb=" C SER A 413 " pdb=" N THR A 414 " pdb=" CA THR A 414 " ideal model delta harmonic sigma weight residual 180.00 149.33 30.67 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA ASP A 430 " pdb=" C ASP A 430 " pdb=" N ASP A 431 " pdb=" CA ASP A 431 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ARG A 375 " pdb=" C ARG A 375 " pdb=" N LYS A 376 " pdb=" CA LYS A 376 " ideal model delta harmonic sigma weight residual 180.00 -155.59 -24.41 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 5423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 791 0.051 - 0.101: 162 0.101 - 0.152: 44 0.152 - 0.202: 2 0.202 - 0.253: 1 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CA ILE A 412 " pdb=" N ILE A 412 " pdb=" C ILE A 412 " pdb=" CB ILE A 412 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ASN A 549 " pdb=" N ASN A 549 " pdb=" C ASN A 549 " pdb=" CB ASN A 549 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE A 327 " pdb=" N ILE A 327 " pdb=" C ILE A 327 " pdb=" CB ILE A 327 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 997 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 411 " 0.016 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" N ILE A 412 " -0.052 2.00e-02 2.50e+03 pdb=" CA ILE A 412 " 0.013 2.00e-02 2.50e+03 pdb=" H ILE A 412 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 443 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C ILE A 443 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 443 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP A 444 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 979 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 980 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 980 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 980 " 0.020 5.00e-02 4.00e+02 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 240 2.16 - 2.77: 18049 2.77 - 3.38: 25824 3.38 - 3.99: 34236 3.99 - 4.60: 53500 Nonbonded interactions: 131849 Sorted by model distance: nonbonded pdb=" H GLU A 794 " pdb=" HA GLU A 794 " model vdw 1.549 1.816 nonbonded pdb=" H VAL A 888 " pdb=" HA VAL A 888 " model vdw 1.569 1.816 nonbonded pdb=" H SER A 828 " pdb=" HA SER A 828 " model vdw 1.580 1.816 nonbonded pdb=" H LYS A 887 " pdb=" HA LYS A 887 " model vdw 1.604 1.816 nonbonded pdb=" O2B ADP A1101 " pdb=" F3 ALF A1102 " model vdw 1.641 2.870 ... (remaining 131844 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: 0.870 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: 0.170 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 35.190 Find NCS groups from input model: 0.090 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.007 0.150 6353 Z= 0.290 Angle : 1.588 71.197 8694 Z= 0.648 Chirality : 0.045 0.253 1000 Planarity : 0.004 0.036 991 Dihedral : 13.469 76.406 2657 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -4.26 (0.26), residues: 679 helix: -1.67 (0.24), residues: 325 sheet: -3.44 (0.45), residues: 75 loop : -4.07 (0.28), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 582 HIS 0.008 0.002 HIS A 928 PHE 0.011 0.002 PHE A 935 TYR 0.020 0.002 TYR A 696 ARG 0.007 0.001 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.12098 ( 299) hydrogen bonds : angle 5.95346 ( 833) metal coordination : bond 0.09425 ( 4) metal coordination : angle 21.03276 ( 6) covalent geometry : bond 0.00619 ( 6349) covalent geometry : angle 1.48965 ( 8688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 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 195 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.897 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 374 PHE cc_start: 0.7411 (t80) cc_final: 0.7077 (t80) REVERT: A 579 TYR cc_start: 0.8516 (t80) cc_final: 0.8068 (t80) REVERT: A 689 LYS cc_start: 0.9148 (mmpt) cc_final: 0.8895 (mmtm) REVERT: A 968 TRP cc_start: 0.7386 (m-10) cc_final: 0.6626 (m-10) REVERT: A 975 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8006 (tttm) REVERT: A 1002 LYS cc_start: 0.8198 (pttt) cc_final: 0.7882 (pttt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.4235 time to fit residues: 103.0062 Evaluate side-chains 110 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN A 784 ASN A 895 GLN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081755 restraints weight = 40517.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.085141 restraints weight = 18499.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087283 restraints weight = 10832.471| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6353 Z= 0.116 Angle : 1.051 30.049 8694 Z= 0.468 Chirality : 0.039 0.173 1000 Planarity : 0.004 0.039 991 Dihedral : 15.137 73.704 1212 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.97 (0.29), residues: 679 helix: -0.35 (0.27), residues: 322 sheet: -2.92 (0.51), residues: 74 loop : -3.72 (0.29), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 968 HIS 0.005 0.001 HIS A 752 PHE 0.013 0.001 PHE A 675 TYR 0.016 0.001 TYR A 869 ARG 0.005 0.001 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 299) hydrogen bonds : angle 4.55085 ( 833) metal coordination : bond 0.00502 ( 4) metal coordination : angle 6.37304 ( 6) covalent geometry : bond 0.00252 ( 6349) covalent geometry : angle 1.03834 ( 8688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 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 142 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.808 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 374 PHE cc_start: 0.7762 (t80) cc_final: 0.7488 (t80) REVERT: A 519 ILE cc_start: 0.7666 (mm) cc_final: 0.7445 (mt) REVERT: A 538 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8135 (mmtt) REVERT: A 592 LYS cc_start: 0.8441 (mttt) cc_final: 0.8034 (tttp) REVERT: A 883 GLU cc_start: 0.8406 (tt0) cc_final: 0.7885 (tm-30) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3837 time to fit residues: 70.3316 Evaluate side-chains 104 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- 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 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077755 restraints weight = 41629.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.081036 restraints weight = 18627.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083116 restraints weight = 10844.631| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6353 Z= 0.140 Angle : 1.040 29.749 8694 Z= 0.461 Chirality : 0.038 0.144 1000 Planarity : 0.003 0.033 991 Dihedral : 14.801 73.481 1212 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.01 (0.31), residues: 679 helix: 0.58 (0.28), residues: 332 sheet: -2.80 (0.50), residues: 76 loop : -3.44 (0.31), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 968 HIS 0.004 0.001 HIS A 626 PHE 0.011 0.001 PHE A 574 TYR 0.017 0.002 TYR A 462 ARG 0.004 0.001 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 299) hydrogen bonds : angle 4.20828 ( 833) metal coordination : bond 0.00572 ( 4) metal coordination : angle 6.41438 ( 6) covalent geometry : bond 0.00291 ( 6349) covalent geometry : angle 1.02705 ( 8688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 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 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7391 (mmmt) REVERT: A 368 MET cc_start: 0.6979 (ptp) cc_final: 0.6574 (ptm) REVERT: A 538 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8264 (mmtt) REVERT: A 580 GLU cc_start: 0.9062 (tt0) cc_final: 0.8648 (tm-30) REVERT: A 592 LYS cc_start: 0.8413 (mttt) cc_final: 0.8048 (tttp) REVERT: A 677 MET cc_start: 0.8565 (mpp) cc_final: 0.8232 (mpp) REVERT: A 687 LEU cc_start: 0.8727 (mt) cc_final: 0.8239 (mt) REVERT: A 689 LYS cc_start: 0.9378 (mmpt) cc_final: 0.9080 (mmtm) REVERT: A 816 MET cc_start: 0.8496 (tmm) cc_final: 0.8210 (tmm) REVERT: A 883 GLU cc_start: 0.8467 (tt0) cc_final: 0.7933 (tm-30) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3215 time to fit residues: 57.9015 Evaluate side-chains 99 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN A 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.072551 restraints weight = 43177.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.075745 restraints weight = 19435.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077803 restraints weight = 11391.237| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6353 Z= 0.213 Angle : 1.063 29.707 8694 Z= 0.481 Chirality : 0.040 0.146 1000 Planarity : 0.004 0.038 991 Dihedral : 14.695 73.369 1212 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.54 % Favored : 91.31 % Rotamer: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.68 (0.31), residues: 679 helix: 0.90 (0.28), residues: 331 sheet: -2.27 (0.55), residues: 76 loop : -3.48 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.006 0.002 HIS A 927 PHE 0.013 0.002 PHE A 374 TYR 0.013 0.002 TYR A 807 ARG 0.006 0.001 ARG A 822 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 299) hydrogen bonds : angle 4.23959 ( 833) metal coordination : bond 0.00962 ( 4) metal coordination : angle 4.91536 ( 6) covalent geometry : bond 0.00436 ( 6349) covalent geometry : angle 1.05535 ( 8688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 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 120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.904 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: A 502 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 580 GLU cc_start: 0.9169 (tt0) cc_final: 0.8815 (tp30) REVERT: A 592 LYS cc_start: 0.8570 (mttt) cc_final: 0.8157 (tttp) REVERT: A 677 MET cc_start: 0.8365 (mpp) cc_final: 0.7915 (mpp) REVERT: A 686 MET cc_start: 0.8037 (ppp) cc_final: 0.7831 (ppp) REVERT: A 687 LEU cc_start: 0.8772 (mt) cc_final: 0.8292 (mt) REVERT: A 919 ASN cc_start: 0.8457 (m110) cc_final: 0.8241 (m-40) REVERT: A 923 ILE cc_start: 0.8666 (tp) cc_final: 0.8246 (tp) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.3109 time to fit residues: 50.3223 Evaluate side-chains 81 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.071998 restraints weight = 43434.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.075080 restraints weight = 19625.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077096 restraints weight = 11594.331| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6353 Z= 0.166 Angle : 1.032 30.908 8694 Z= 0.461 Chirality : 0.038 0.146 1000 Planarity : 0.003 0.027 991 Dihedral : 14.547 73.460 1212 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.36 (0.31), residues: 679 helix: 1.21 (0.28), residues: 331 sheet: -2.14 (0.55), residues: 76 loop : -3.37 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.005 0.001 HIS A 928 PHE 0.009 0.001 PHE A 935 TYR 0.012 0.002 TYR A 579 ARG 0.003 0.001 ARG A 822 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 299) hydrogen bonds : angle 4.09474 ( 833) metal coordination : bond 0.00190 ( 4) metal coordination : angle 3.93709 ( 6) covalent geometry : bond 0.00342 ( 6349) covalent geometry : angle 1.02723 ( 8688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 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 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.937 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: A 459 MET cc_start: 0.9199 (mmp) cc_final: 0.8751 (mmp) REVERT: A 502 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 580 GLU cc_start: 0.9168 (tt0) cc_final: 0.8856 (tp30) REVERT: A 592 LYS cc_start: 0.8558 (mttt) cc_final: 0.8104 (tttp) REVERT: A 677 MET cc_start: 0.8430 (mpp) cc_final: 0.7921 (mpp) REVERT: A 687 LEU cc_start: 0.8823 (mt) cc_final: 0.8302 (mt) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.3255 time to fit residues: 48.9014 Evaluate side-chains 76 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.089283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072627 restraints weight = 43337.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075855 restraints weight = 19293.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077970 restraints weight = 11271.429| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6353 Z= 0.110 Angle : 1.006 29.783 8694 Z= 0.445 Chirality : 0.038 0.143 1000 Planarity : 0.003 0.029 991 Dihedral : 14.465 73.550 1212 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.05 (0.32), residues: 679 helix: 1.37 (0.28), residues: 339 sheet: -2.01 (0.55), residues: 75 loop : -3.20 (0.33), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 582 HIS 0.004 0.001 HIS A 928 PHE 0.006 0.001 PHE A 681 TYR 0.007 0.001 TYR A 312 ARG 0.003 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 299) hydrogen bonds : angle 3.84654 ( 833) metal coordination : bond 0.00252 ( 4) metal coordination : angle 3.76980 ( 6) covalent geometry : bond 0.00228 ( 6349) covalent geometry : angle 1.00137 ( 8688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 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 108 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.804 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: A 459 MET cc_start: 0.9153 (mmp) cc_final: 0.8731 (mmp) REVERT: A 580 GLU cc_start: 0.9147 (tt0) cc_final: 0.8836 (tp30) REVERT: A 592 LYS cc_start: 0.8565 (mttt) cc_final: 0.8315 (mtpp) REVERT: A 677 MET cc_start: 0.8338 (mpp) cc_final: 0.7803 (mpp) REVERT: A 770 GLU cc_start: 0.8791 (mp0) cc_final: 0.8452 (mp0) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.2720 time to fit residues: 40.9504 Evaluate side-chains 80 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN A 615 ASN ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.068809 restraints weight = 44502.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.071846 restraints weight = 19738.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073824 restraints weight = 11576.135| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 6353 Z= 0.247 Angle : 1.068 30.194 8694 Z= 0.487 Chirality : 0.041 0.133 1000 Planarity : 0.004 0.042 991 Dihedral : 14.559 73.422 1212 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.30 (0.32), residues: 679 helix: 1.16 (0.28), residues: 337 sheet: -1.99 (0.55), residues: 75 loop : -3.34 (0.32), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 582 HIS 0.006 0.002 HIS A 974 PHE 0.013 0.002 PHE A 374 TYR 0.013 0.002 TYR A 579 ARG 0.008 0.001 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 299) hydrogen bonds : angle 4.21399 ( 833) metal coordination : bond 0.00823 ( 4) metal coordination : angle 2.99269 ( 6) covalent geometry : bond 0.00504 ( 6349) covalent geometry : angle 1.06547 ( 8688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 1.048 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: A 394 ASP cc_start: 0.7349 (p0) cc_final: 0.7136 (p0) REVERT: A 459 MET cc_start: 0.9345 (mmp) cc_final: 0.9031 (mmp) REVERT: A 580 GLU cc_start: 0.9261 (tt0) cc_final: 0.8682 (tm-30) REVERT: A 677 MET cc_start: 0.8491 (mpp) cc_final: 0.7879 (mpp) REVERT: A 770 GLU cc_start: 0.8890 (mp0) cc_final: 0.8419 (mp0) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.2901 time to fit residues: 40.9715 Evaluate side-chains 76 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.0170 chunk 55 optimal weight: 0.7980 chunk 17 optimal weight: 0.0570 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN A 784 ASN A 974 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.072847 restraints weight = 43331.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.075948 restraints weight = 19179.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077989 restraints weight = 11221.750| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6353 Z= 0.088 Angle : 1.000 29.750 8694 Z= 0.441 Chirality : 0.038 0.147 1000 Planarity : 0.003 0.030 991 Dihedral : 14.430 73.661 1212 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.74 (0.33), residues: 679 helix: 1.77 (0.28), residues: 332 sheet: -1.81 (0.54), residues: 81 loop : -3.18 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 582 HIS 0.004 0.001 HIS A 928 PHE 0.011 0.001 PHE A 639 TYR 0.011 0.001 TYR A 869 ARG 0.003 0.001 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 299) hydrogen bonds : angle 3.65156 ( 833) metal coordination : bond 0.00260 ( 4) metal coordination : angle 2.61381 ( 6) covalent geometry : bond 0.00189 ( 6349) covalent geometry : angle 0.99780 ( 8688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 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 108 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.892 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: A 459 MET cc_start: 0.9136 (mmp) cc_final: 0.8862 (mmp) REVERT: A 592 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8754 (mtpp) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.2796 time to fit residues: 42.3702 Evaluate side-chains 79 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** 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 = 0.3307 r_free = 0.3307 target = 0.086138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.069884 restraints weight = 44728.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.072971 restraints weight = 19606.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.074992 restraints weight = 11423.672| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6353 Z= 0.178 Angle : 1.027 29.838 8694 Z= 0.462 Chirality : 0.039 0.138 1000 Planarity : 0.003 0.034 991 Dihedral : 14.495 73.544 1212 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.16 % Allowed : 0.49 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.81 (0.32), residues: 679 helix: 1.71 (0.28), residues: 332 sheet: -1.66 (0.56), residues: 75 loop : -3.26 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 582 HIS 0.004 0.001 HIS A 447 PHE 0.011 0.001 PHE A 374 TYR 0.014 0.001 TYR A 579 ARG 0.003 0.001 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 299) hydrogen bonds : angle 3.90196 ( 833) metal coordination : bond 0.00584 ( 4) metal coordination : angle 2.24819 ( 6) covalent geometry : bond 0.00363 ( 6349) covalent geometry : angle 1.02590 ( 8688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.865 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: A 459 MET cc_start: 0.9215 (mmp) cc_final: 0.8907 (mmp) REVERT: A 559 MET cc_start: 0.8751 (ttt) cc_final: 0.8423 (tpt) REVERT: A 677 MET cc_start: 0.8422 (mpp) cc_final: 0.7863 (mpp) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.2915 time to fit residues: 40.8503 Evaluate side-chains 73 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN A 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.072744 restraints weight = 43655.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.075877 restraints weight = 19282.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077966 restraints weight = 11243.965| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6353 Z= 0.087 Angle : 0.997 29.846 8694 Z= 0.440 Chirality : 0.037 0.145 1000 Planarity : 0.003 0.031 991 Dihedral : 14.418 73.693 1212 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.46 (0.33), residues: 679 helix: 2.05 (0.28), residues: 326 sheet: -1.47 (0.55), residues: 81 loop : -3.09 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 582 HIS 0.004 0.001 HIS A 928 PHE 0.010 0.001 PHE A 639 TYR 0.013 0.001 TYR A 579 ARG 0.004 0.000 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.02885 ( 299) hydrogen bonds : angle 3.58419 ( 833) metal coordination : bond 0.00245 ( 4) metal coordination : angle 2.10668 ( 6) covalent geometry : bond 0.00184 ( 6349) covalent geometry : angle 0.99531 ( 8688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 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 104 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.893 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: A 459 MET cc_start: 0.9021 (mmp) cc_final: 0.8652 (mmp) REVERT: A 677 MET cc_start: 0.8362 (mpp) cc_final: 0.7879 (mpp) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.3133 time to fit residues: 44.3664 Evaluate side-chains 81 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.086860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.070658 restraints weight = 44137.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073789 restraints weight = 19771.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.075845 restraints weight = 11564.081| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6353 Z= 0.152 Angle : 1.016 29.707 8694 Z= 0.454 Chirality : 0.038 0.137 1000 Planarity : 0.003 0.030 991 Dihedral : 14.455 73.597 1212 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 679 helix: 1.94 (0.28), residues: 326 sheet: -1.36 (0.55), residues: 81 loop : -3.12 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 582 HIS 0.007 0.001 HIS A 626 PHE 0.009 0.001 PHE A 639 TYR 0.011 0.001 TYR A 608 ARG 0.003 0.001 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.03094 ( 299) hydrogen bonds : angle 3.77642 ( 833) metal coordination : bond 0.00458 ( 4) metal coordination : angle 1.78517 ( 6) covalent geometry : bond 0.00313 ( 6349) covalent geometry : angle 1.01495 ( 8688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3633.59 seconds wall clock time: 63 minutes 6.26 seconds (3786.26 seconds total)