Starting phenix.real_space_refine on Sun Jun 8 17:30:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wf9_37487/06_2025/8wf9_37487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wf9_37487/06_2025/8wf9_37487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wf9_37487/06_2025/8wf9_37487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wf9_37487/06_2025/8wf9_37487.map" model { file = "/net/cci-nas-00/data/ceres_data/8wf9_37487/06_2025/8wf9_37487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wf9_37487/06_2025/8wf9_37487.cif" } resolution = 3.13 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= 0.038 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: 6 Type Number sf(0) Gaussians P 72 5.49 5 Mg 1 5.21 5 S 42 5.16 5 C 5961 2.51 5 N 1697 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 8276 Classifications: {'peptide': 1002} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 969} Chain breaks: 10 Chain: "B" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1148 Classifications: {'RNA': 54} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 23, 'rna3p_pyr': 25} Link IDs: {'rna2p': 6, 'rna3p': 47} Chain: "C" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 391 Classifications: {'RNA': 18} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.57, per 1000 atoms: 0.67 Number of scatterers: 9816 At special positions: 0 Unit cell: (101.26, 104.58, 127.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 72 15.00 Mg 1 11.99 O 2043 8.00 N 1697 7.00 C 5961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 65.5% alpha, 7.6% beta 30 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 10 through 36 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.521A pdb=" N LYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 63 " --> pdb=" O TYR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 83 Processing helix chain 'A' and resid 84 through 97 removed outlier: 4.488A pdb=" N ILE A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 151 through 175 removed outlier: 3.637A pdb=" N VAL A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 removed outlier: 4.851A pdb=" N PHE A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 236 removed outlier: 4.010A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.541A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.810A pdb=" N LYS A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 518 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 537 through 546 Processing helix chain 'A' and resid 552 through 577 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.077A pdb=" N PHE A 655 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.805A pdb=" N VAL A 675 " --> pdb=" O PHE A 671 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 676' Processing helix chain 'A' and resid 683 through 708 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 739 Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.577A pdb=" N LEU A 760 " --> pdb=" O HIS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 764 Processing helix chain 'A' and resid 767 through 771 removed outlier: 4.026A pdb=" N ALA A 771 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.549A pdb=" N ALA A 778 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 821 through 831 Processing helix chain 'A' and resid 831 through 849 Processing helix chain 'A' and resid 858 through 904 removed outlier: 3.714A pdb=" N VAL A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 924 through 927 Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 956 through 963 removed outlier: 3.537A pdb=" N VAL A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 975 Processing helix chain 'A' and resid 981 through 1013 Proline residue: A 996 - end of helix Processing helix chain 'A' and resid 1014 through 1022 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1042 through 1058 Processing helix chain 'A' and resid 1074 through 1087 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 190 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213 Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283 removed outlier: 5.713A pdb=" N MET A 930 " --> pdb=" O GLY A 949 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A 949 " --> pdb=" O MET A 930 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 389 removed outlier: 4.256A pdb=" N GLY A 360 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A 388 " --> pdb=" O ASN A 358 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN A 358 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 414 removed outlier: 4.093A pdb=" N LYS A 361 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU A 447 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N ASN A 358 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 15.981A pdb=" N LYS A 445 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 462 through 464 removed outlier: 3.710A pdb=" N VAL A 462 " --> pdb=" O VAL A 470 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1581 1.32 - 1.45: 3009 1.45 - 1.57: 5333 1.57 - 1.69: 146 1.69 - 1.82: 78 Bond restraints: 10147 Sorted by residual: bond pdb=" CA ALA A 485 " pdb=" CB ALA A 485 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.11e+01 bond pdb=" CA PRO A 484 " pdb=" CB PRO A 484 " ideal model delta sigma weight residual 1.534 1.485 0.049 1.52e-02 4.33e+03 1.04e+01 bond pdb=" C ASP A 890 " pdb=" O ASP A 890 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.17e-02 7.31e+03 9.77e+00 bond pdb=" CA SER A 475 " pdb=" CB SER A 475 " ideal model delta sigma weight residual 1.528 1.482 0.047 1.56e-02 4.11e+03 8.96e+00 bond pdb=" CA VAL A 714 " pdb=" CB VAL A 714 " ideal model delta sigma weight residual 1.539 1.555 -0.016 5.40e-03 3.43e+04 8.87e+00 ... (remaining 10142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 13110 3.35 - 6.70: 775 6.70 - 10.04: 87 10.04 - 13.39: 10 13.39 - 16.74: 3 Bond angle restraints: 13985 Sorted by residual: angle pdb=" C3' G B 10 " pdb=" C2' G B 10 " pdb=" O2' G B 10 " ideal model delta sigma weight residual 110.70 125.05 -14.35 1.50e+00 4.44e-01 9.16e+01 angle pdb=" CA ARG A 835 " pdb=" CB ARG A 835 " pdb=" CG ARG A 835 " ideal model delta sigma weight residual 114.10 129.74 -15.64 2.00e+00 2.50e-01 6.12e+01 angle pdb=" O3' A B 29 " pdb=" P U B 30 " pdb=" O5' U B 30 " ideal model delta sigma weight residual 104.00 92.40 11.60 1.50e+00 4.44e-01 5.98e+01 angle pdb=" CG MET A 763 " pdb=" SD MET A 763 " pdb=" CE MET A 763 " ideal model delta sigma weight residual 100.90 117.64 -16.74 2.20e+00 2.07e-01 5.79e+01 angle pdb=" CA PHE A 671 " pdb=" CB PHE A 671 " pdb=" CG PHE A 671 " ideal model delta sigma weight residual 113.80 121.22 -7.42 1.00e+00 1.00e+00 5.50e+01 ... (remaining 13980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5519 17.43 - 34.85: 516 34.85 - 52.28: 145 52.28 - 69.71: 113 69.71 - 87.13: 24 Dihedral angle restraints: 6317 sinusoidal: 3357 harmonic: 2960 Sorted by residual: dihedral pdb=" C5' G B 21 " pdb=" C4' G B 21 " pdb=" C3' G B 21 " pdb=" O3' G B 21 " ideal model delta sinusoidal sigma weight residual 147.00 100.10 46.90 1 8.00e+00 1.56e-02 4.75e+01 dihedral pdb=" C LYS A 782 " pdb=" N LYS A 782 " pdb=" CA LYS A 782 " pdb=" CB LYS A 782 " ideal model delta harmonic sigma weight residual -122.60 -139.70 17.10 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" O4' G B 21 " pdb=" C4' G B 21 " pdb=" C3' G B 21 " pdb=" C2' G B 21 " ideal model delta sinusoidal sigma weight residual 24.00 -21.91 45.91 1 8.00e+00 1.56e-02 4.56e+01 ... (remaining 6314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1260 0.121 - 0.242: 292 0.242 - 0.362: 14 0.362 - 0.483: 4 0.483 - 0.604: 4 Chirality restraints: 1574 Sorted by residual: chirality pdb=" CA LYS A 782 " pdb=" N LYS A 782 " pdb=" C LYS A 782 " pdb=" CB LYS A 782 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" P U C 1 " pdb=" OP1 U C 1 " pdb=" OP2 U C 1 " pdb=" O5' U C 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" P U B -17 " pdb=" OP1 U B -17 " pdb=" OP2 U B -17 " pdb=" O5' U B -17 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.11e+00 ... (remaining 1571 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 30 " -0.063 2.00e-02 2.50e+03 3.34e-02 2.51e+01 pdb=" N1 U B 30 " 0.062 2.00e-02 2.50e+03 pdb=" C2 U B 30 " 0.014 2.00e-02 2.50e+03 pdb=" O2 U B 30 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U B 30 " 0.021 2.00e-02 2.50e+03 pdb=" C4 U B 30 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U B 30 " -0.029 2.00e-02 2.50e+03 pdb=" C5 U B 30 " -0.010 2.00e-02 2.50e+03 pdb=" C6 U B 30 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 19 " -0.054 2.00e-02 2.50e+03 3.20e-02 2.31e+01 pdb=" N1 U B 19 " 0.067 2.00e-02 2.50e+03 pdb=" C2 U B 19 " 0.009 2.00e-02 2.50e+03 pdb=" O2 U B 19 " -0.013 2.00e-02 2.50e+03 pdb=" N3 U B 19 " 0.014 2.00e-02 2.50e+03 pdb=" C4 U B 19 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 19 " -0.022 2.00e-02 2.50e+03 pdb=" C5 U B 19 " -0.024 2.00e-02 2.50e+03 pdb=" C6 U B 19 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 8 " -0.055 2.00e-02 2.50e+03 2.79e-02 2.14e+01 pdb=" N9 A B 8 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A B 8 " 0.015 2.00e-02 2.50e+03 pdb=" N7 A B 8 " 0.032 2.00e-02 2.50e+03 pdb=" C5 A B 8 " -0.020 2.00e-02 2.50e+03 pdb=" C6 A B 8 " -0.029 2.00e-02 2.50e+03 pdb=" N6 A B 8 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A B 8 " -0.013 2.00e-02 2.50e+03 pdb=" C2 A B 8 " 0.030 2.00e-02 2.50e+03 pdb=" N3 A B 8 " 0.023 2.00e-02 2.50e+03 pdb=" C4 A B 8 " -0.009 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 232 2.68 - 3.24: 8897 3.24 - 3.79: 15710 3.79 - 4.35: 21986 4.35 - 4.90: 33177 Nonbonded interactions: 80002 Sorted by model distance: nonbonded pdb=" OE1 GLN A 747 " pdb="MG MG A1101 " model vdw 2.129 2.170 nonbonded pdb=" OD2 ASP A 345 " pdb=" OH TYR A 439 " model vdw 2.135 3.040 nonbonded pdb=" OG SER A 259 " pdb=" OE1 GLU A 261 " model vdw 2.199 3.040 nonbonded pdb=" OP1 G B 23 " pdb="MG MG A1101 " model vdw 2.205 2.170 nonbonded pdb=" O2' U B 18 " pdb=" OP2 G B 21 " model vdw 2.290 3.040 ... (remaining 79997 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: 6.040 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 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 : 0.010 0.069 10147 Z= 0.583 Angle : 1.784 16.739 13985 Z= 1.119 Chirality : 0.098 0.604 1574 Planarity : 0.007 0.071 1530 Dihedral : 17.420 87.133 4395 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.53 % Favored : 98.37 % Rotamer: Outliers : 3.07 % Allowed : 5.93 % Favored : 91.00 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 6.45 % 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: -1.03 (0.24), residues: 980 helix: -1.10 (0.17), residues: 568 sheet: 0.39 (0.82), residues: 44 loop : 0.26 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.006 TRP A 829 HIS 0.013 0.003 HIS A 756 PHE 0.041 0.006 PHE A 355 TYR 0.051 0.007 TYR A 343 ARG 0.049 0.004 ARG A 835 Details of bonding type rmsd hydrogen bonds : bond 0.18634 ( 551) hydrogen bonds : angle 6.77911 ( 1475) covalent geometry : bond 0.00966 (10147) covalent geometry : angle 1.78424 (13985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.954 Fit side-chains REVERT: A 1 MET cc_start: 0.7281 (ttp) cc_final: 0.7029 (tmm) REVERT: A 10 GLN cc_start: 0.7764 (mm110) cc_final: 0.7319 (mp10) REVERT: A 96 TYR cc_start: 0.8132 (t80) cc_final: 0.7847 (t80) REVERT: A 132 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7934 (m-40) REVERT: A 139 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: A 171 ASN cc_start: 0.7025 (t0) cc_final: 0.6565 (m-40) REVERT: A 176 TYR cc_start: 0.7238 (m-80) cc_final: 0.6939 (m-80) REVERT: A 186 ASP cc_start: 0.7538 (m-30) cc_final: 0.7296 (t70) REVERT: A 187 LYS cc_start: 0.7004 (mttt) cc_final: 0.6601 (mmtp) REVERT: A 365 LEU cc_start: 0.6662 (tt) cc_final: 0.6238 (tp) REVERT: A 393 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6462 (tp30) REVERT: A 453 LYS cc_start: 0.8076 (mttt) cc_final: 0.7762 (tptt) REVERT: A 516 MET cc_start: 0.7109 (mtp) cc_final: 0.6742 (mtp) REVERT: A 519 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6234 (mp0) REVERT: A 520 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5235 (tm-30) REVERT: A 534 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 547 ASN cc_start: 0.7860 (m-40) cc_final: 0.7502 (m110) REVERT: A 730 LYS cc_start: 0.7441 (tttt) cc_final: 0.6593 (ptpt) REVERT: A 738 GLU cc_start: 0.7600 (pt0) cc_final: 0.7206 (pt0) REVERT: A 927 SER cc_start: 0.7705 (t) cc_final: 0.7275 (m) REVERT: A 965 LYS cc_start: 0.8433 (mttt) cc_final: 0.8210 (tttt) REVERT: A 1007 LYS cc_start: 0.8060 (tttt) cc_final: 0.7834 (tttp) REVERT: A 1008 TRP cc_start: 0.7689 (t60) cc_final: 0.7370 (t60) REVERT: A 1013 TYR cc_start: 0.8567 (m-80) cc_final: 0.7642 (m-10) REVERT: A 1027 ASP cc_start: 0.8125 (t0) cc_final: 0.7847 (t0) REVERT: A 1038 ASN cc_start: 0.8421 (m-40) cc_final: 0.7752 (t0) REVERT: A 1047 ASP cc_start: 0.8068 (m-30) cc_final: 0.7738 (t0) REVERT: A 1061 TYR cc_start: 0.8775 (m-80) cc_final: 0.8377 (m-80) REVERT: A 1077 MET cc_start: 0.7705 (mmm) cc_final: 0.7296 (mmt) outliers start: 28 outliers final: 12 residues processed: 216 average time/residue: 0.2665 time to fit residues: 76.1249 Evaluate side-chains 138 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 907 PHE Chi-restraints excluded: chain A residue 1020 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 153 GLN A 169 ASN A 171 ASN A 219 GLN A 358 ASN A 387 ASN A 514 GLN A 756 HIS A 794 GLN A 852 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.200004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148021 restraints weight = 11201.136| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.39 r_work: 0.3369 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10147 Z= 0.136 Angle : 0.541 5.755 13985 Z= 0.292 Chirality : 0.038 0.200 1574 Planarity : 0.004 0.042 1530 Dihedral : 16.665 78.532 2267 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.41 % Allowed : 10.10 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.69 (0.26), residues: 980 helix: 1.76 (0.20), residues: 576 sheet: 0.38 (0.81), residues: 44 loop : 0.29 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 724 HIS 0.004 0.001 HIS A 489 PHE 0.017 0.001 PHE A 792 TYR 0.018 0.002 TYR A 886 ARG 0.006 0.001 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.05468 ( 551) hydrogen bonds : angle 4.13598 ( 1475) covalent geometry : bond 0.00281 (10147) covalent geometry : angle 0.54053 (13985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.043 Fit side-chains REVERT: A 96 TYR cc_start: 0.8007 (t80) cc_final: 0.7761 (t80) REVERT: A 126 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7713 (ttp) REVERT: A 129 ASP cc_start: 0.8092 (m-30) cc_final: 0.7841 (m-30) REVERT: A 170 MET cc_start: 0.7071 (mtp) cc_final: 0.6583 (mtp) REVERT: A 187 LYS cc_start: 0.7790 (mttt) cc_final: 0.7564 (mmtp) REVERT: A 297 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: A 365 LEU cc_start: 0.6893 (tt) cc_final: 0.6631 (tp) REVERT: A 453 LYS cc_start: 0.8477 (mttt) cc_final: 0.8191 (mtmm) REVERT: A 520 GLU cc_start: 0.6364 (mt-10) cc_final: 0.5472 (tm-30) REVERT: A 763 MET cc_start: 0.8402 (mmm) cc_final: 0.8120 (mmm) REVERT: A 1013 TYR cc_start: 0.8571 (m-80) cc_final: 0.8136 (m-10) REVERT: A 1038 ASN cc_start: 0.8257 (m-40) cc_final: 0.7787 (t0) outliers start: 22 outliers final: 9 residues processed: 140 average time/residue: 0.2351 time to fit residues: 45.7818 Evaluate side-chains 111 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 0.0980 chunk 50 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 38 optimal weight: 0.0870 chunk 100 optimal weight: 30.0000 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 153 GLN A 219 GLN A 517 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.202236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150065 restraints weight = 11484.742| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.38 r_work: 0.3363 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10147 Z= 0.106 Angle : 0.451 5.159 13985 Z= 0.242 Chirality : 0.035 0.143 1574 Planarity : 0.003 0.037 1530 Dihedral : 16.416 74.028 2245 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.20 % Allowed : 10.21 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.39 (0.27), residues: 980 helix: 2.37 (0.21), residues: 584 sheet: 0.72 (0.84), residues: 41 loop : 0.44 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1008 HIS 0.003 0.001 HIS A 57 PHE 0.017 0.001 PHE A 513 TYR 0.014 0.001 TYR A 127 ARG 0.005 0.000 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 551) hydrogen bonds : angle 3.81787 ( 1475) covalent geometry : bond 0.00215 (10147) covalent geometry : angle 0.45144 (13985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.028 Fit side-chains REVERT: A 1 MET cc_start: 0.8233 (ttp) cc_final: 0.7770 (tmm) REVERT: A 129 ASP cc_start: 0.8142 (m-30) cc_final: 0.7924 (m-30) REVERT: A 187 LYS cc_start: 0.7870 (mttt) cc_final: 0.7564 (mmtp) REVERT: A 297 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: A 365 LEU cc_start: 0.6712 (tt) cc_final: 0.6222 (tp) REVERT: A 453 LYS cc_start: 0.8523 (mttt) cc_final: 0.8202 (mtmm) REVERT: A 520 GLU cc_start: 0.6402 (mt-10) cc_final: 0.5547 (tm-30) REVERT: A 738 GLU cc_start: 0.8206 (pt0) cc_final: 0.7962 (pt0) REVERT: A 781 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6923 (ttt) REVERT: A 1013 TYR cc_start: 0.8490 (m-80) cc_final: 0.7900 (m-80) REVERT: A 1038 ASN cc_start: 0.8088 (m-40) cc_final: 0.7738 (t0) outliers start: 20 outliers final: 11 residues processed: 130 average time/residue: 0.2348 time to fit residues: 42.9749 Evaluate side-chains 114 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 982 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.198730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144055 restraints weight = 11360.097| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.56 r_work: 0.3303 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10147 Z= 0.156 Angle : 0.496 6.682 13985 Z= 0.261 Chirality : 0.037 0.166 1574 Planarity : 0.004 0.035 1530 Dihedral : 16.429 74.064 2244 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.52 % Allowed : 12.18 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.34 (0.27), residues: 980 helix: 2.36 (0.21), residues: 576 sheet: 0.48 (0.85), residues: 41 loop : 0.43 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1008 HIS 0.004 0.001 HIS A 489 PHE 0.036 0.002 PHE A 513 TYR 0.024 0.002 TYR A 736 ARG 0.006 0.001 ARG A 800 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 551) hydrogen bonds : angle 3.87004 ( 1475) covalent geometry : bond 0.00360 (10147) covalent geometry : angle 0.49575 (13985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.905 Fit side-chains REVERT: A 105 ARG cc_start: 0.6505 (ptp90) cc_final: 0.6040 (ptt-90) REVERT: A 187 LYS cc_start: 0.8013 (mttt) cc_final: 0.7670 (mmtp) REVERT: A 297 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: A 365 LEU cc_start: 0.6764 (tt) cc_final: 0.6303 (tp) REVERT: A 453 LYS cc_start: 0.8638 (mttt) cc_final: 0.8183 (mtmt) REVERT: A 520 GLU cc_start: 0.6470 (mt-10) cc_final: 0.5667 (tm-30) REVERT: A 763 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8222 (mtm) REVERT: A 781 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7171 (ttt) REVERT: A 831 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6913 (mt-10) REVERT: A 853 MET cc_start: 0.7133 (mmm) cc_final: 0.6912 (mmt) REVERT: A 1013 TYR cc_start: 0.8463 (m-80) cc_final: 0.8024 (m-80) REVERT: A 1038 ASN cc_start: 0.8053 (m-40) cc_final: 0.7656 (t0) outliers start: 23 outliers final: 16 residues processed: 120 average time/residue: 0.2617 time to fit residues: 44.4284 Evaluate side-chains 114 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.200013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145850 restraints weight = 11261.397| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.46 r_work: 0.3346 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10147 Z= 0.104 Angle : 0.439 5.866 13985 Z= 0.233 Chirality : 0.035 0.140 1574 Planarity : 0.003 0.033 1530 Dihedral : 16.296 73.949 2241 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.87 % Allowed : 12.40 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.59 (0.27), residues: 980 helix: 2.57 (0.21), residues: 575 sheet: 0.71 (0.87), residues: 41 loop : 0.52 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1008 HIS 0.003 0.001 HIS A 57 PHE 0.023 0.001 PHE A 513 TYR 0.015 0.001 TYR A 736 ARG 0.005 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 551) hydrogen bonds : angle 3.73955 ( 1475) covalent geometry : bond 0.00226 (10147) covalent geometry : angle 0.43883 (13985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.041 Fit side-chains REVERT: A 105 ARG cc_start: 0.6462 (ptp90) cc_final: 0.5843 (ptt-90) REVERT: A 187 LYS cc_start: 0.8040 (mttt) cc_final: 0.7671 (mmtp) REVERT: A 297 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: A 365 LEU cc_start: 0.6716 (tt) cc_final: 0.6301 (tp) REVERT: A 453 LYS cc_start: 0.8625 (mttt) cc_final: 0.8315 (mtmt) REVERT: A 520 GLU cc_start: 0.6450 (mt-10) cc_final: 0.5681 (tm-30) REVERT: A 738 GLU cc_start: 0.8156 (pt0) cc_final: 0.7902 (pt0) REVERT: A 831 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6946 (mt-10) REVERT: A 1013 TYR cc_start: 0.8408 (m-80) cc_final: 0.8092 (m-10) REVERT: A 1038 ASN cc_start: 0.8018 (m-40) cc_final: 0.7611 (t0) outliers start: 17 outliers final: 11 residues processed: 114 average time/residue: 0.2475 time to fit residues: 38.9103 Evaluate side-chains 111 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 976 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.197787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143306 restraints weight = 11401.630| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.59 r_work: 0.3301 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10147 Z= 0.142 Angle : 0.472 6.384 13985 Z= 0.247 Chirality : 0.036 0.153 1574 Planarity : 0.004 0.034 1530 Dihedral : 16.274 73.973 2241 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.31 % Allowed : 12.29 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.44 (0.27), residues: 980 helix: 2.45 (0.21), residues: 576 sheet: 0.54 (0.84), residues: 46 loop : 0.45 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1008 HIS 0.003 0.001 HIS A 489 PHE 0.019 0.001 PHE A 513 TYR 0.014 0.001 TYR A 17 ARG 0.003 0.000 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 551) hydrogen bonds : angle 3.77596 ( 1475) covalent geometry : bond 0.00332 (10147) covalent geometry : angle 0.47214 (13985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.115 Fit side-chains REVERT: A 94 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7625 (ttp80) REVERT: A 105 ARG cc_start: 0.6518 (ptp90) cc_final: 0.5892 (ptt-90) REVERT: A 187 LYS cc_start: 0.8145 (mttt) cc_final: 0.7720 (mmtp) REVERT: A 248 ARG cc_start: 0.8722 (mmt90) cc_final: 0.8510 (mmt-90) REVERT: A 297 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: A 365 LEU cc_start: 0.6800 (tt) cc_final: 0.6368 (tp) REVERT: A 453 LYS cc_start: 0.8679 (mttt) cc_final: 0.8346 (mtmt) REVERT: A 520 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5691 (tm-30) REVERT: A 564 MET cc_start: 0.6016 (mtp) cc_final: 0.5789 (mmm) REVERT: A 738 GLU cc_start: 0.8190 (pt0) cc_final: 0.7939 (pt0) REVERT: A 831 GLU cc_start: 0.7232 (mt-10) cc_final: 0.7018 (mt-10) REVERT: A 937 GLU cc_start: 0.7612 (tt0) cc_final: 0.7370 (mt-10) REVERT: A 942 LYS cc_start: 0.7625 (tttt) cc_final: 0.7418 (mttm) outliers start: 21 outliers final: 17 residues processed: 120 average time/residue: 0.3335 time to fit residues: 54.4414 Evaluate side-chains 114 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 976 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 chunk 54 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 514 GLN A 722 ASN A1040 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.196310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140885 restraints weight = 11562.811| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.69 r_work: 0.3288 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10147 Z= 0.164 Angle : 0.500 8.994 13985 Z= 0.259 Chirality : 0.037 0.165 1574 Planarity : 0.004 0.038 1530 Dihedral : 16.280 74.050 2241 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.63 % Allowed : 12.18 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.34 (0.27), residues: 980 helix: 2.36 (0.21), residues: 577 sheet: 0.33 (0.83), residues: 48 loop : 0.46 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1008 HIS 0.004 0.001 HIS A 489 PHE 0.017 0.002 PHE A 792 TYR 0.014 0.002 TYR A 17 ARG 0.006 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.04428 ( 551) hydrogen bonds : angle 3.85540 ( 1475) covalent geometry : bond 0.00386 (10147) covalent geometry : angle 0.50009 (13985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.142 Fit side-chains REVERT: A 87 LYS cc_start: 0.7434 (mttt) cc_final: 0.6950 (mtpp) REVERT: A 94 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7582 (ttp80) REVERT: A 105 ARG cc_start: 0.6595 (ptp90) cc_final: 0.5940 (ptt-90) REVERT: A 187 LYS cc_start: 0.8204 (mttt) cc_final: 0.7793 (mmtp) REVERT: A 297 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: A 365 LEU cc_start: 0.6823 (tt) cc_final: 0.6396 (tp) REVERT: A 453 LYS cc_start: 0.8737 (mttt) cc_final: 0.8231 (mtmm) REVERT: A 520 GLU cc_start: 0.6496 (mt-10) cc_final: 0.5684 (tm-30) REVERT: A 564 MET cc_start: 0.5884 (mtp) cc_final: 0.5660 (mmm) REVERT: A 831 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 937 GLU cc_start: 0.7609 (tt0) cc_final: 0.7376 (mt-10) REVERT: A 942 LYS cc_start: 0.7670 (tttt) cc_final: 0.7408 (mttm) REVERT: A 1013 TYR cc_start: 0.8126 (m-10) cc_final: 0.7920 (m-80) outliers start: 24 outliers final: 20 residues processed: 124 average time/residue: 0.2811 time to fit residues: 48.1512 Evaluate side-chains 116 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 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 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.196795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142196 restraints weight = 11513.073| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.61 r_work: 0.3293 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10147 Z= 0.147 Angle : 0.482 7.383 13985 Z= 0.251 Chirality : 0.036 0.158 1574 Planarity : 0.004 0.034 1530 Dihedral : 16.234 73.972 2241 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.41 % Allowed : 12.62 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.39 (0.27), residues: 980 helix: 2.41 (0.21), residues: 577 sheet: 0.28 (0.83), residues: 48 loop : 0.47 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1008 HIS 0.004 0.001 HIS A 489 PHE 0.017 0.001 PHE A 792 TYR 0.014 0.001 TYR A 17 ARG 0.008 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 551) hydrogen bonds : angle 3.80574 ( 1475) covalent geometry : bond 0.00345 (10147) covalent geometry : angle 0.48228 (13985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.059 Fit side-chains REVERT: A 87 LYS cc_start: 0.7444 (mttt) cc_final: 0.6977 (mtpp) REVERT: A 94 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7594 (ttp80) REVERT: A 105 ARG cc_start: 0.6627 (ptp90) cc_final: 0.5986 (ptt-90) REVERT: A 187 LYS cc_start: 0.8227 (mttt) cc_final: 0.7810 (mmtp) REVERT: A 297 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: A 365 LEU cc_start: 0.6856 (tt) cc_final: 0.6426 (tp) REVERT: A 453 LYS cc_start: 0.8751 (mttt) cc_final: 0.8245 (mtmm) REVERT: A 520 GLU cc_start: 0.6526 (mt-10) cc_final: 0.5697 (tm-30) REVERT: A 564 MET cc_start: 0.5964 (mtp) cc_final: 0.5704 (mmm) REVERT: A 831 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 937 GLU cc_start: 0.7664 (tt0) cc_final: 0.7448 (mt-10) REVERT: A 942 LYS cc_start: 0.7721 (tttt) cc_final: 0.7412 (ttmm) outliers start: 22 outliers final: 19 residues processed: 116 average time/residue: 0.2528 time to fit residues: 40.2385 Evaluate side-chains 115 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 984 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 105 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 722 ASN A1038 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.197976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143890 restraints weight = 11487.873| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.69 r_work: 0.3303 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10147 Z= 0.128 Angle : 0.462 7.806 13985 Z= 0.240 Chirality : 0.035 0.146 1574 Planarity : 0.004 0.034 1530 Dihedral : 16.171 73.872 2241 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.41 % Allowed : 13.17 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.51 (0.27), residues: 980 helix: 2.51 (0.21), residues: 577 sheet: 0.33 (0.83), residues: 48 loop : 0.52 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1008 HIS 0.003 0.001 HIS A 489 PHE 0.016 0.001 PHE A 792 TYR 0.013 0.001 TYR A 17 ARG 0.008 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 551) hydrogen bonds : angle 3.74462 ( 1475) covalent geometry : bond 0.00298 (10147) covalent geometry : angle 0.46233 (13985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.972 Fit side-chains REVERT: A 87 LYS cc_start: 0.7510 (mttt) cc_final: 0.7054 (mtpp) REVERT: A 94 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7755 (ttp-170) REVERT: A 105 ARG cc_start: 0.6524 (ptp90) cc_final: 0.5845 (ptt-90) REVERT: A 187 LYS cc_start: 0.8252 (mttt) cc_final: 0.7828 (mmtp) REVERT: A 297 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: A 365 LEU cc_start: 0.6839 (tt) cc_final: 0.6422 (tp) REVERT: A 453 LYS cc_start: 0.8783 (mttt) cc_final: 0.8270 (mtmm) REVERT: A 520 GLU cc_start: 0.6488 (mt-10) cc_final: 0.5670 (tm-30) REVERT: A 564 MET cc_start: 0.5995 (mtp) cc_final: 0.5706 (mmm) REVERT: A 831 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 937 GLU cc_start: 0.7660 (tt0) cc_final: 0.7415 (mt-10) REVERT: A 942 LYS cc_start: 0.7721 (tttt) cc_final: 0.7440 (mttm) REVERT: A 1077 MET cc_start: 0.8211 (mmt) cc_final: 0.7864 (mmt) outliers start: 22 outliers final: 18 residues processed: 121 average time/residue: 0.2610 time to fit residues: 43.7812 Evaluate side-chains 118 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 976 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 95 optimal weight: 0.0370 chunk 62 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 219 GLN A 722 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.198537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144655 restraints weight = 11445.788| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.53 r_work: 0.3328 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10147 Z= 0.121 Angle : 0.463 10.331 13985 Z= 0.239 Chirality : 0.035 0.142 1574 Planarity : 0.004 0.034 1530 Dihedral : 16.157 73.858 2241 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.31 % Allowed : 13.28 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.58 (0.27), residues: 980 helix: 2.56 (0.21), residues: 577 sheet: 0.37 (0.84), residues: 48 loop : 0.55 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1008 HIS 0.003 0.001 HIS A 57 PHE 0.016 0.001 PHE A 792 TYR 0.013 0.001 TYR A 17 ARG 0.007 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 551) hydrogen bonds : angle 3.71855 ( 1475) covalent geometry : bond 0.00279 (10147) covalent geometry : angle 0.46302 (13985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.7495 (mttt) cc_final: 0.7047 (mtpp) REVERT: A 94 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7748 (ttp-170) REVERT: A 105 ARG cc_start: 0.6527 (ptp90) cc_final: 0.5852 (ptt-90) REVERT: A 187 LYS cc_start: 0.8230 (mttt) cc_final: 0.7825 (mmtp) REVERT: A 297 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: A 365 LEU cc_start: 0.6827 (tt) cc_final: 0.6431 (tp) REVERT: A 453 LYS cc_start: 0.8771 (mttt) cc_final: 0.8260 (mtmm) REVERT: A 520 GLU cc_start: 0.6471 (mt-10) cc_final: 0.5507 (tm-30) REVERT: A 564 MET cc_start: 0.5971 (mtp) cc_final: 0.5697 (mmm) REVERT: A 831 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6965 (mt-10) REVERT: A 937 GLU cc_start: 0.7636 (tt0) cc_final: 0.7398 (mt-10) REVERT: A 942 LYS cc_start: 0.7742 (tttt) cc_final: 0.7462 (mttm) REVERT: A 1077 MET cc_start: 0.8169 (mmt) cc_final: 0.7860 (mmt) outliers start: 21 outliers final: 17 residues processed: 118 average time/residue: 0.2619 time to fit residues: 42.2419 Evaluate side-chains 117 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 976 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 18 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 722 ASN A 845 ASN A1038 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.200272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146344 restraints weight = 11401.179| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.43 r_work: 0.3354 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10147 Z= 0.100 Angle : 0.433 7.950 13985 Z= 0.226 Chirality : 0.034 0.133 1574 Planarity : 0.004 0.034 1530 Dihedral : 16.097 73.850 2241 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.20 % Allowed : 13.50 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.75 (0.27), residues: 980 helix: 2.71 (0.21), residues: 576 sheet: 0.39 (0.83), residues: 48 loop : 0.62 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1008 HIS 0.003 0.000 HIS A 57 PHE 0.015 0.001 PHE A 792 TYR 0.012 0.001 TYR A 17 ARG 0.008 0.000 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 551) hydrogen bonds : angle 3.62046 ( 1475) covalent geometry : bond 0.00223 (10147) covalent geometry : angle 0.43297 (13985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5690.89 seconds wall clock time: 100 minutes 27.94 seconds (6027.94 seconds total)