Starting phenix.real_space_refine on Sun Dec 29 08:57:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wb0_32391/12_2024/7wb0_32391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb0_32391/12_2024/7wb0_32391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wb0_32391/12_2024/7wb0_32391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb0_32391/12_2024/7wb0_32391.map" model { file = "/net/cci-nas-00/data/ceres_data/7wb0_32391/12_2024/7wb0_32391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb0_32391/12_2024/7wb0_32391.cif" } resolution = 3.2 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= -0.000 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 175 5.49 5 S 24 5.16 5 C 5765 2.51 5 N 1804 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10096 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 674 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 55, 'rna3p_pyr': 47} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain breaks: 1 Chain: "A" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6429 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 35, 'TRANS': 761} Chain breaks: 4 Time building chain proxies: 6.37, per 1000 atoms: 0.63 Number of scatterers: 10096 At special positions: 0 Unit cell: (104.34, 141, 125.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 175 15.00 O 2328 8.00 N 1804 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 912 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 955.1 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 40.8% alpha, 18.4% beta 55 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 60 through 92 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.618A pdb=" N LEU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.533A pdb=" N HIS A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 221 through 272 removed outlier: 3.662A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 647 through 650 removed outlier: 3.590A pdb=" N ILE A 650 " --> pdb=" O SER A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 697 through 717 removed outlier: 3.645A pdb=" N LYS A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 removed outlier: 3.539A pdb=" N ARG A 774 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 790 removed outlier: 3.998A pdb=" N GLU A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 821 through 829 removed outlier: 3.681A pdb=" N VAL A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 881 through 885 removed outlier: 3.596A pdb=" N SER A 884 " --> pdb=" O ASP A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 898 Processing helix chain 'A' and resid 921 through 936 removed outlier: 3.569A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 removed outlier: 3.649A pdb=" N LYS A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 950 " --> pdb=" O THR A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 973 removed outlier: 3.708A pdb=" N VAL A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.928A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU A 611 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU A 640 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 613 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.988A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 128 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.988A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N THR A 153 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.671A pdb=" N LYS A 544 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 571 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL A 559 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 517 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ASN A 561 " --> pdb=" O CYS A 515 " (cutoff:3.500A) removed outlier: 12.726A pdb=" N CYS A 515 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 516 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 694 removed outlier: 3.663A pdb=" N ALA A 666 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A 654 " --> pdb=" O MET A 752 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 754 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 656 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ALA A 756 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ILE A 658 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR A 801 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 755 " --> pdb=" O THR A 801 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AA8, first strand: chain 'A' and resid 831 through 832 removed outlier: 3.551A pdb=" N THR A 838 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855 removed outlier: 3.583A pdb=" N TYR A 853 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 862 " --> pdb=" O TYR A 853 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 909 through 911 298 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2062 1.33 - 1.45: 3183 1.45 - 1.57: 5025 1.57 - 1.69: 346 1.69 - 1.81: 36 Bond restraints: 10652 Sorted by residual: bond pdb=" CA ASP A 522 " pdb=" CB ASP A 522 " ideal model delta sigma weight residual 1.522 1.539 -0.017 1.27e-02 6.20e+03 1.88e+00 bond pdb=" C ALA A 320 " pdb=" N LYS A 321 " ideal model delta sigma weight residual 1.331 1.357 -0.026 2.07e-02 2.33e+03 1.63e+00 bond pdb=" C LYS A 210 " pdb=" O LYS A 210 " ideal model delta sigma weight residual 1.249 1.239 0.010 8.50e-03 1.38e+04 1.45e+00 bond pdb=" CG GLN A 702 " pdb=" CD GLN A 702 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CA ASN A 528 " pdb=" C ASN A 528 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.08e-02 8.57e+03 1.35e+00 ... (remaining 10647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 14949 2.09 - 4.18: 207 4.18 - 6.27: 16 6.27 - 8.35: 2 8.35 - 10.44: 1 Bond angle restraints: 15175 Sorted by residual: angle pdb=" C LYS A 899 " pdb=" N ARG A 900 " pdb=" CA ARG A 900 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C LYS A 701 " pdb=" N GLN A 702 " pdb=" CA GLN A 702 " ideal model delta sigma weight residual 120.72 115.48 5.24 1.67e+00 3.59e-01 9.83e+00 angle pdb=" C LEU A 529 " pdb=" N TYR A 530 " pdb=" CA TYR A 530 " ideal model delta sigma weight residual 121.87 126.97 -5.10 1.64e+00 3.72e-01 9.67e+00 angle pdb=" C PHE A 901 " pdb=" N SER A 902 " pdb=" CA SER A 902 " ideal model delta sigma weight residual 122.56 117.92 4.64 1.50e+00 4.44e-01 9.58e+00 angle pdb=" N GLN A 702 " pdb=" CA GLN A 702 " pdb=" CB GLN A 702 " ideal model delta sigma weight residual 110.39 115.51 -5.12 1.66e+00 3.63e-01 9.53e+00 ... (remaining 15170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 5699 29.54 - 59.07: 599 59.07 - 88.61: 128 88.61 - 118.14: 2 118.14 - 147.68: 1 Dihedral angle restraints: 6429 sinusoidal: 4103 harmonic: 2326 Sorted by residual: dihedral pdb=" O4' U D 17 " pdb=" C1' U D 17 " pdb=" N1 U D 17 " pdb=" C2 U D 17 " ideal model delta sinusoidal sigma weight residual 232.00 84.32 147.68 1 1.70e+01 3.46e-03 6.13e+01 dihedral pdb=" CA HIS A 903 " pdb=" C HIS A 903 " pdb=" N ARG A 904 " pdb=" CA ARG A 904 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 333 " pdb=" C PRO A 333 " pdb=" N LEU A 334 " pdb=" CA LEU A 334 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 6426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1355 0.033 - 0.067: 313 0.067 - 0.100: 72 0.100 - 0.133: 36 0.133 - 0.166: 2 Chirality restraints: 1778 Sorted by residual: chirality pdb=" CB THR A 953 " pdb=" CA THR A 953 " pdb=" OG1 THR A 953 " pdb=" CG2 THR A 953 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CB ILE A 114 " pdb=" CA ILE A 114 " pdb=" CG1 ILE A 114 " pdb=" CG2 ILE A 114 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA VAL A 667 " pdb=" N VAL A 667 " pdb=" C VAL A 667 " pdb=" CB VAL A 667 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1775 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 889 " 0.164 9.50e-02 1.11e+02 7.37e-02 3.41e+00 pdb=" NE ARG A 889 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 889 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 889 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 889 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 20 " 0.020 2.00e-02 2.50e+03 1.04e-02 2.44e+00 pdb=" N1 U D 20 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U D 20 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U D 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U D 20 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U D 20 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U D 20 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U D 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U D 20 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 38 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 39 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.021 5.00e-02 4.00e+02 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 394 2.69 - 3.24: 8735 3.24 - 3.79: 16669 3.79 - 4.35: 20645 4.35 - 4.90: 31638 Nonbonded interactions: 78081 Sorted by model distance: nonbonded pdb=" OD1 ASP A 733 " pdb=" ND2 ASN A 737 " model vdw 2.136 3.120 nonbonded pdb=" OG1 THR A 38 " pdb=" OD1 ASP A 40 " model vdw 2.198 3.040 nonbonded pdb=" O6 DG B 22 " pdb=" NZ LYS A 227 " model vdw 2.246 3.120 nonbonded pdb=" O2 U D 45 " pdb=" N4 C D 46 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN A 737 " pdb=" NH2 ARG A 740 " model vdw 2.257 3.120 ... (remaining 78076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10652 Z= 0.155 Angle : 0.579 10.444 15175 Z= 0.323 Chirality : 0.034 0.166 1778 Planarity : 0.004 0.074 1303 Dihedral : 21.369 147.677 4922 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 0.54 (0.31), residues: 787 helix: 2.01 (0.30), residues: 297 sheet: 0.14 (0.46), residues: 134 loop : -1.01 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 304 HIS 0.001 0.001 HIS A 920 PHE 0.006 0.001 PHE A 917 TYR 0.016 0.001 TYR A 698 ARG 0.005 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.878 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2377 time to fit residues: 22.1161 Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 804 GLN A 812 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10652 Z= 0.159 Angle : 0.540 6.769 15175 Z= 0.289 Chirality : 0.034 0.152 1778 Planarity : 0.004 0.046 1303 Dihedral : 23.296 148.477 3268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 0.57 % Allowed : 6.29 % Favored : 93.14 % 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 (0.31), residues: 787 helix: 2.22 (0.30), residues: 304 sheet: 0.37 (0.48), residues: 123 loop : -0.91 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 304 HIS 0.002 0.001 HIS A 173 PHE 0.008 0.001 PHE A 588 TYR 0.017 0.001 TYR A 244 ARG 0.003 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.871 Fit side-chains REVERT: A 141 LYS cc_start: 0.6986 (ttmt) cc_final: 0.6644 (ttpt) REVERT: A 627 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7111 (mtt-85) REVERT: A 709 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7271 (tttm) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.3122 time to fit residues: 23.4828 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10652 Z= 0.257 Angle : 0.597 7.936 15175 Z= 0.319 Chirality : 0.037 0.164 1778 Planarity : 0.005 0.057 1303 Dihedral : 23.289 137.350 3268 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % Rotamer: Outliers : 1.00 % Allowed : 9.71 % Favored : 89.29 % 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: 0.44 (0.30), residues: 787 helix: 2.10 (0.30), residues: 298 sheet: -0.22 (0.45), residues: 135 loop : -1.11 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 86 HIS 0.003 0.001 HIS A 920 PHE 0.014 0.002 PHE A 588 TYR 0.025 0.002 TYR A 244 ARG 0.013 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 141 LYS cc_start: 0.7124 (ttmt) cc_final: 0.6922 (ttpp) REVERT: A 247 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7396 (tp) REVERT: A 627 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7151 (mtt-85) REVERT: A 660 ARG cc_start: 0.5740 (mtm180) cc_final: 0.4550 (ttm110) REVERT: A 709 LYS cc_start: 0.7841 (ttmt) cc_final: 0.7450 (tttt) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 0.2861 time to fit residues: 23.1752 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10652 Z= 0.346 Angle : 0.677 8.525 15175 Z= 0.361 Chirality : 0.040 0.151 1778 Planarity : 0.005 0.059 1303 Dihedral : 23.431 131.611 3268 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.97 % Favored : 93.90 % Rotamer: Outliers : 2.29 % Allowed : 12.14 % Favored : 85.57 % 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: -0.05 (0.30), residues: 787 helix: 1.66 (0.30), residues: 298 sheet: -0.56 (0.45), residues: 133 loop : -1.31 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 836 HIS 0.008 0.002 HIS A 251 PHE 0.019 0.002 PHE A 815 TYR 0.027 0.002 TYR A 244 ARG 0.009 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 247 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7485 (tp) REVERT: A 618 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 627 ARG cc_start: 0.7504 (mtt90) cc_final: 0.7146 (mtt-85) REVERT: A 660 ARG cc_start: 0.5756 (mtm180) cc_final: 0.4495 (ttm110) REVERT: A 709 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8105 (tttt) REVERT: A 775 GLN cc_start: 0.7575 (mp10) cc_final: 0.7315 (mp10) REVERT: A 776 TYR cc_start: 0.5082 (OUTLIER) cc_final: 0.2974 (m-80) outliers start: 16 outliers final: 4 residues processed: 68 average time/residue: 0.3040 time to fit residues: 27.5296 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 962 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10652 Z= 0.168 Angle : 0.554 8.082 15175 Z= 0.300 Chirality : 0.035 0.135 1778 Planarity : 0.004 0.049 1303 Dihedral : 23.274 135.145 3268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 1.43 % Allowed : 14.57 % Favored : 84.00 % 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: 0.35 (0.31), residues: 787 helix: 2.09 (0.30), residues: 298 sheet: -0.39 (0.46), residues: 132 loop : -1.16 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 304 HIS 0.002 0.001 HIS A 173 PHE 0.010 0.001 PHE A 332 TYR 0.018 0.001 TYR A 244 ARG 0.007 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.840 Fit side-chains REVERT: A 310 TRP cc_start: 0.6071 (m-10) cc_final: 0.5824 (m-10) REVERT: A 618 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 627 ARG cc_start: 0.7410 (mtt90) cc_final: 0.7088 (mtt-85) REVERT: A 660 ARG cc_start: 0.5803 (mtm180) cc_final: 0.4464 (ttm110) REVERT: A 754 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8015 (mp) REVERT: A 776 TYR cc_start: 0.4974 (OUTLIER) cc_final: 0.2853 (m-80) outliers start: 10 outliers final: 4 residues processed: 62 average time/residue: 0.2959 time to fit residues: 24.9103 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 776 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10652 Z= 0.212 Angle : 0.573 8.114 15175 Z= 0.309 Chirality : 0.036 0.138 1778 Planarity : 0.004 0.050 1303 Dihedral : 23.287 135.687 3268 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Rotamer: Outliers : 1.71 % Allowed : 15.14 % Favored : 83.14 % 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: 0.37 (0.31), residues: 787 helix: 2.13 (0.30), residues: 299 sheet: -0.50 (0.45), residues: 135 loop : -1.13 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 304 HIS 0.003 0.001 HIS A 920 PHE 0.012 0.001 PHE A 588 TYR 0.020 0.002 TYR A 244 ARG 0.008 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 1.038 Fit side-chains REVERT: A 310 TRP cc_start: 0.6114 (m-10) cc_final: 0.5840 (m-10) REVERT: A 618 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 627 ARG cc_start: 0.7385 (mtt90) cc_final: 0.7074 (mtt-85) REVERT: A 660 ARG cc_start: 0.5819 (mtm180) cc_final: 0.4674 (ttm110) REVERT: A 754 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7879 (mp) REVERT: A 776 TYR cc_start: 0.5077 (OUTLIER) cc_final: 0.3034 (m-80) outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.2900 time to fit residues: 22.9771 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 813 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10652 Z= 0.153 Angle : 0.532 7.701 15175 Z= 0.289 Chirality : 0.034 0.135 1778 Planarity : 0.004 0.047 1303 Dihedral : 23.201 138.308 3268 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.43 % Allowed : 16.29 % Favored : 82.29 % 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: 0.52 (0.31), residues: 787 helix: 2.11 (0.30), residues: 305 sheet: -0.33 (0.46), residues: 135 loop : -0.99 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 304 HIS 0.002 0.001 HIS A 920 PHE 0.009 0.001 PHE A 332 TYR 0.015 0.001 TYR A 244 ARG 0.008 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.865 Fit side-chains REVERT: A 247 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7440 (tp) REVERT: A 618 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 627 ARG cc_start: 0.7338 (mtt90) cc_final: 0.7049 (mtt-85) REVERT: A 660 ARG cc_start: 0.5748 (mtm180) cc_final: 0.4502 (ttm110) REVERT: A 754 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 776 TYR cc_start: 0.4936 (OUTLIER) cc_final: 0.2858 (m-80) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.3059 time to fit residues: 21.6015 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 776 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.5980 chunk 27 optimal weight: 0.0270 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10652 Z= 0.147 Angle : 0.522 7.553 15175 Z= 0.282 Chirality : 0.034 0.131 1778 Planarity : 0.004 0.048 1303 Dihedral : 23.134 139.891 3268 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 1.57 % Allowed : 16.29 % Favored : 82.14 % 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: 0.66 (0.31), residues: 787 helix: 2.26 (0.30), residues: 305 sheet: -0.37 (0.45), residues: 137 loop : -0.90 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 304 HIS 0.002 0.001 HIS A 920 PHE 0.009 0.001 PHE A 588 TYR 0.014 0.001 TYR A 244 ARG 0.007 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.880 Fit side-chains REVERT: A 247 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7431 (tp) REVERT: A 618 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7179 (tm-30) REVERT: A 627 ARG cc_start: 0.7433 (mtt90) cc_final: 0.7128 (mtt-85) REVERT: A 660 ARG cc_start: 0.5712 (mtm180) cc_final: 0.4499 (ttm110) REVERT: A 776 TYR cc_start: 0.4905 (OUTLIER) cc_final: 0.2994 (m-80) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 0.3065 time to fit residues: 23.6104 Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 698 TYR Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 784 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10652 Z= 0.161 Angle : 0.532 7.796 15175 Z= 0.286 Chirality : 0.034 0.130 1778 Planarity : 0.004 0.043 1303 Dihedral : 23.113 140.448 3268 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 1.14 % Allowed : 16.86 % Favored : 82.00 % 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: 0.59 (0.32), residues: 787 helix: 2.27 (0.30), residues: 305 sheet: -0.65 (0.43), residues: 147 loop : -0.88 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 304 HIS 0.002 0.001 HIS A 920 PHE 0.010 0.001 PHE A 588 TYR 0.015 0.001 TYR A 244 ARG 0.004 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.915 Fit side-chains REVERT: A 247 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7446 (tp) REVERT: A 618 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7178 (tm-30) REVERT: A 627 ARG cc_start: 0.7466 (mtt90) cc_final: 0.7118 (mtt-85) REVERT: A 660 ARG cc_start: 0.5744 (mtm180) cc_final: 0.4475 (ttm110) REVERT: A 754 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8043 (mp) REVERT: A 776 TYR cc_start: 0.4886 (OUTLIER) cc_final: 0.2988 (m-80) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.3116 time to fit residues: 21.4869 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 776 TYR Chi-restraints excluded: chain A residue 784 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 0.3980 chunk 94 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 80 optimal weight: 0.0670 chunk 23 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10652 Z= 0.134 Angle : 0.510 8.088 15175 Z= 0.274 Chirality : 0.033 0.141 1778 Planarity : 0.004 0.045 1303 Dihedral : 23.065 144.337 3268 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 0.57 % Allowed : 17.43 % Favored : 82.00 % 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: 0.71 (0.32), residues: 787 helix: 2.36 (0.30), residues: 305 sheet: -0.57 (0.43), residues: 147 loop : -0.81 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 304 HIS 0.001 0.001 HIS A 690 PHE 0.007 0.001 PHE A 332 TYR 0.011 0.001 TYR A 244 ARG 0.006 0.000 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.944 Fit side-chains REVERT: A 618 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 627 ARG cc_start: 0.7438 (mtt90) cc_final: 0.7071 (mtt-85) REVERT: A 660 ARG cc_start: 0.5640 (mtm180) cc_final: 0.4686 (ttm110) REVERT: A 754 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 776 TYR cc_start: 0.4718 (OUTLIER) cc_final: 0.2870 (m-80) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.3140 time to fit residues: 19.7644 Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 776 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.167657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.120423 restraints weight = 21673.782| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.23 r_work: 0.3484 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10652 Z= 0.293 Angle : 0.616 8.054 15175 Z= 0.329 Chirality : 0.038 0.173 1778 Planarity : 0.004 0.046 1303 Dihedral : 23.243 135.515 3268 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % Rotamer: Outliers : 0.71 % Allowed : 17.14 % Favored : 82.14 % 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: 0.28 (0.31), residues: 787 helix: 2.10 (0.30), residues: 299 sheet: -0.95 (0.42), residues: 147 loop : -1.01 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 304 HIS 0.004 0.001 HIS A 920 PHE 0.015 0.002 PHE A 588 TYR 0.025 0.002 TYR A 244 ARG 0.005 0.001 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.59 seconds wall clock time: 37 minutes 10.75 seconds (2230.75 seconds total)