Starting phenix.real_space_refine on Thu Jul 2 18:38:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ewg_28645/07_2026/8ewg_28645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ewg_28645/07_2026/8ewg_28645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ewg_28645/07_2026/8ewg_28645.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ewg_28645/07_2026/8ewg_28645.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ewg_28645/07_2026/8ewg_28645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ewg_28645/07_2026/8ewg_28645.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ewg_28645/07_2026/8ewg_28645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ewg_28645/07_2026/8ewg_28645.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 55 5.49 5 S 36 5.16 5 C 5861 2.51 5 N 1720 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9616 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 8423 Classifications: {'peptide': 1017} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 990} Chain breaks: 4 Chain: "B" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1193 Inner-chain residues flagged as termini: ['pdbres=" A B 52 "'] Classifications: {'RNA': 56} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 34} Time building chain proxies: 2.00, per 1000 atoms: 0.21 Number of scatterers: 9616 At special positions: 0 Unit cell: (79.05, 102, 107.1, 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 36 16.00 P 55 15.00 O 1944 8.00 N 1720 7.00 C 5861 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: 0.83 Conformation dependent library (CDL) restraints added in 274.9 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 68.8% alpha, 1.7% beta 8 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.661A pdb=" N ALA A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.560A pdb=" N GLY A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 249 through 272 Processing helix chain 'A' and resid 275 through 294 removed outlier: 4.162A pdb=" N TYR A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 321 through 347 removed outlier: 3.510A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 394 Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.740A pdb=" N ASP A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 453 Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.999A pdb=" N ILE A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 475 through 497 Processing helix chain 'A' and resid 505 through 517 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 535 through 548 removed outlier: 4.030A pdb=" N ALA A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.623A pdb=" N TYR A 553 " --> pdb=" O PRO A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 581 through 607 removed outlier: 3.619A pdb=" N VAL A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 674 removed outlier: 3.545A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 683 through 700 removed outlier: 3.506A pdb=" N THR A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 689 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.704A pdb=" N GLU A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A 721 " --> pdb=" O ILE A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 749 Processing helix chain 'A' and resid 754 through 777 removed outlier: 3.643A pdb=" N ARG A 758 " --> pdb=" O ASP A 754 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.827A pdb=" N ALA A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 827 Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 831 through 850 Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 892 through 899 removed outlier: 5.892A pdb=" N ASP A 897 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 898 " --> pdb=" O PHE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.578A pdb=" N GLU A 907 " --> pdb=" O LYS A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 930 removed outlier: 3.708A pdb=" N SER A 930 " --> pdb=" O ARG A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 940 Processing helix chain 'A' and resid 948 through 955 Processing helix chain 'A' and resid 971 through 989 Processing helix chain 'A' and resid 994 through 1019 removed outlier: 3.742A pdb=" N GLU A1002 " --> pdb=" O CYS A 998 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1034 Processing helix chain 'A' and resid 1036 through 1058 Processing helix chain 'A' and resid 1065 through 1073 removed outlier: 3.649A pdb=" N PHE A1073 " --> pdb=" O VAL A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1086 Processing helix chain 'A' and resid 1088 through 1096 removed outlier: 3.563A pdb=" N ASN A1092 " --> pdb=" O GLY A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1116 removed outlier: 4.086A pdb=" N ASN A1112 " --> pdb=" O LEU A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1125 removed outlier: 5.939A pdb=" N LYS A1122 " --> pdb=" O LEU A1119 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN A1123 " --> pdb=" O MET A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1148 Processing helix chain 'A' and resid 1150 through 1167 removed outlier: 4.536A pdb=" N THR A1158 " --> pdb=" O MET A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1221 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA3, first strand: chain 'A' and resid 1173 through 1176 removed outlier: 6.703A pdb=" N ARG A1173 " --> pdb=" O GLU A1185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1191 through 1193 476 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 1.08 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: 2026 1.33 - 1.45: 2513 1.45 - 1.58: 5203 1.58 - 1.70: 109 1.70 - 1.82: 59 Bond restraints: 9910 Sorted by residual: bond pdb=" CA ARG A 992 " pdb=" CB ARG A 992 " ideal model delta sigma weight residual 1.526 1.572 -0.046 1.53e-02 4.27e+03 8.88e+00 bond pdb=" C PHE A1099 " pdb=" N PRO A1100 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.26e+00 bond pdb=" O5' C B 47 " pdb=" C5' C B 47 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.33e+00 bond pdb=" CA VAL A1221 " pdb=" CB VAL A1221 " ideal model delta sigma weight residual 1.531 1.551 -0.020 1.11e-02 8.12e+03 3.12e+00 bond pdb=" C TYR A1222 " pdb=" N PRO A1223 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.45e+00 ... (remaining 9905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 13273 2.28 - 4.55: 259 4.55 - 6.83: 45 6.83 - 9.10: 11 9.10 - 11.38: 4 Bond angle restraints: 13592 Sorted by residual: angle pdb=" CA THR A 802 " pdb=" CB THR A 802 " pdb=" CG2 THR A 802 " ideal model delta sigma weight residual 110.50 117.42 -6.92 1.70e+00 3.46e-01 1.66e+01 angle pdb=" C PHE A 909 " pdb=" N TYR A 910 " pdb=" CA TYR A 910 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" N SER A 362 " pdb=" CA SER A 362 " pdb=" C SER A 362 " ideal model delta sigma weight residual 111.28 115.49 -4.21 1.09e+00 8.42e-01 1.49e+01 angle pdb=" CB MET A1048 " pdb=" CG MET A1048 " pdb=" SD MET A1048 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C4' U B 18 " pdb=" C3' U B 18 " pdb=" O3' U B 18 " ideal model delta sigma weight residual 109.40 114.86 -5.46 1.50e+00 4.44e-01 1.32e+01 ... (remaining 13587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 5604 35.69 - 71.38: 303 71.38 - 107.07: 30 107.07 - 142.76: 1 142.76 - 178.45: 6 Dihedral angle restraints: 5944 sinusoidal: 2948 harmonic: 2996 Sorted by residual: dihedral pdb=" O4' C B 47 " pdb=" C1' C B 47 " pdb=" N1 C B 47 " pdb=" C2 C B 47 " ideal model delta sinusoidal sigma weight residual 200.00 46.21 153.79 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' U B 48 " pdb=" C1' U B 48 " pdb=" N1 U B 48 " pdb=" C2 U B 48 " ideal model delta sinusoidal sigma weight residual 200.00 46.79 153.21 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' C B 35 " pdb=" C1' C B 35 " pdb=" N1 C B 35 " pdb=" C2 C B 35 " ideal model delta sinusoidal sigma weight residual 200.00 50.92 149.08 1 1.50e+01 4.44e-03 7.93e+01 ... (remaining 5941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1307 0.065 - 0.129: 166 0.129 - 0.193: 26 0.193 - 0.258: 3 0.258 - 0.322: 4 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CG LEU A 305 " pdb=" CB LEU A 305 " pdb=" CD1 LEU A 305 " pdb=" CD2 LEU A 305 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB THR A 802 " pdb=" CA THR A 802 " pdb=" OG1 THR A 802 " pdb=" CG2 THR A 802 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1' G B 21 " pdb=" O4' G B 21 " pdb=" C2' G B 21 " pdb=" N9 G B 21 " both_signs ideal model delta sigma weight residual False 2.46 2.17 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1503 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 877 " -0.059 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO A 878 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 878 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 878 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 46 " 0.037 2.00e-02 2.50e+03 1.72e-02 8.13e+00 pdb=" N9 A B 46 " -0.039 2.00e-02 2.50e+03 pdb=" C8 A B 46 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 46 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B 46 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 46 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A B 46 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A B 46 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A B 46 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A B 46 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A B 46 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 843 " 0.013 2.00e-02 2.50e+03 1.66e-02 5.49e+00 pdb=" CG TYR A 843 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 843 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 843 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 843 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 843 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 843 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 843 " -0.004 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1249 2.75 - 3.29: 8803 3.29 - 3.83: 16158 3.83 - 4.36: 18502 4.36 - 4.90: 31292 Nonbonded interactions: 76004 Sorted by model distance: nonbonded pdb=" O2' G B 41 " pdb=" O2 U B 42 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 986 " pdb=" O LYS A1196 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 913 " pdb=" N ASP A 914 " model vdw 2.279 3.120 nonbonded pdb=" O SER A1019 " pdb=" OG SER A1019 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 910 " pdb=" O LEU A1018 " model vdw 2.316 3.040 ... (remaining 75999 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: 0.800 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.004 0.053 9910 Z= 0.207 Angle : 0.810 11.377 13592 Z= 0.434 Chirality : 0.048 0.322 1506 Planarity : 0.006 0.090 1548 Dihedral : 20.771 178.449 4002 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 1.43 % Allowed : 29.09 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.25), residues: 1007 helix: 0.52 (0.19), residues: 654 sheet: -1.03 (0.99), residues: 30 loop : -2.91 (0.29), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 949 TYR 0.041 0.002 TYR A 843 PHE 0.020 0.002 PHE A 909 TRP 0.008 0.002 TRP A1125 HIS 0.007 0.001 HIS A 958 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 ( 9910) covalent geometry : angle 0.81046 / 0.43 (13592) hydrogen bonds : bond 0.15338 / 10.18 ( 497) hydrogen bonds : angle 4.98969 / 3.52 ( 1433) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 425 ASP cc_start: 0.8650 (m-30) cc_final: 0.8329 (m-30) outliers start: 13 outliers final: 2 residues processed: 93 average time/residue: 0.5237 time to fit residues: 52.1641 Evaluate side-chains 74 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 919 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN A 838 GLN A1168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119885 restraints weight = 12755.671| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.34 r_work: 0.3284 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9910 Z= 0.141 Angle : 0.581 6.251 13592 Z= 0.306 Chirality : 0.040 0.229 1506 Planarity : 0.004 0.074 1548 Dihedral : 16.445 178.072 1807 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.40 % Allowed : 27.33 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.27), residues: 1007 helix: 1.68 (0.20), residues: 664 sheet: -1.56 (1.10), residues: 20 loop : -2.51 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 949 TYR 0.013 0.001 TYR A 344 PHE 0.016 0.001 PHE A 909 TRP 0.012 0.001 TRP A 887 HIS 0.004 0.001 HIS A 958 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 9910) covalent geometry : angle 0.58128 / 0.31 (13592) hydrogen bonds : bond 0.06497 / 4.65 ( 497) hydrogen bonds : angle 3.46598 / 2.45 ( 1433) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.254 Fit side-chains REVERT: A 445 LYS cc_start: 0.8513 (tmtm) cc_final: 0.8309 (tmmm) REVERT: A 732 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7471 (ttmt) REVERT: A 733 GLN cc_start: 0.8075 (mt0) cc_final: 0.7762 (mt0) REVERT: A 830 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6292 (pm20) REVERT: A 977 CYS cc_start: 0.7127 (m) cc_final: 0.6869 (m) outliers start: 31 outliers final: 7 residues processed: 108 average time/residue: 0.5571 time to fit residues: 64.0469 Evaluate side-chains 83 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 HIS A 838 GLN A1058 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119161 restraints weight = 12732.803| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.31 r_work: 0.3286 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9910 Z= 0.127 Angle : 0.555 6.760 13592 Z= 0.289 Chirality : 0.039 0.215 1506 Planarity : 0.004 0.060 1548 Dihedral : 16.370 177.983 1803 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.07 % Allowed : 28.76 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.27), residues: 1007 helix: 2.15 (0.20), residues: 667 sheet: -1.16 (0.96), residues: 30 loop : -2.47 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 949 TYR 0.011 0.001 TYR A 344 PHE 0.012 0.001 PHE A 909 TRP 0.018 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 9910) covalent geometry : angle 0.55534 / 0.29 (13592) hydrogen bonds : bond 0.05647 / 4.00 ( 497) hydrogen bonds : angle 3.25162 / 2.31 ( 1433) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8447 (tmtm) cc_final: 0.8237 (tmmm) REVERT: A 718 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: A 732 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7464 (ttmt) REVERT: A 733 GLN cc_start: 0.8155 (mt0) cc_final: 0.7949 (mt0) REVERT: A 830 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: A 977 CYS cc_start: 0.7232 (m) cc_final: 0.6983 (m) REVERT: A 1106 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7861 (tppt) REVERT: A 1214 ASP cc_start: 0.8110 (m-30) cc_final: 0.7851 (m-30) outliers start: 28 outliers final: 6 residues processed: 103 average time/residue: 0.5666 time to fit residues: 62.2078 Evaluate side-chains 81 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 ASN A 838 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116723 restraints weight = 12881.510| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.36 r_work: 0.3242 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9910 Z= 0.146 Angle : 0.570 7.737 13592 Z= 0.297 Chirality : 0.039 0.248 1506 Planarity : 0.004 0.052 1548 Dihedral : 16.432 176.870 1803 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.07 % Allowed : 28.87 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 1007 helix: 2.30 (0.20), residues: 663 sheet: -1.22 (0.94), residues: 30 loop : -2.40 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 949 TYR 0.014 0.001 TYR A 344 PHE 0.015 0.001 PHE A 909 TRP 0.021 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 9910) covalent geometry : angle 0.56986 / 0.30 (13592) hydrogen bonds : bond 0.06139 / 4.34 ( 497) hydrogen bonds : angle 3.23599 / 2.30 ( 1433) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8414 (tmtm) cc_final: 0.8195 (tmmm) REVERT: A 556 ASP cc_start: 0.7818 (p0) cc_final: 0.7612 (p0) REVERT: A 718 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: A 732 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7653 (ttpt) REVERT: A 830 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6326 (pm20) REVERT: A 900 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: A 977 CYS cc_start: 0.7253 (m) cc_final: 0.7012 (m) REVERT: A 1106 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7905 (tppt) REVERT: A 1214 ASP cc_start: 0.8166 (m-30) cc_final: 0.7916 (m-30) REVERT: A 1220 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8509 (mmp) outliers start: 28 outliers final: 11 residues processed: 94 average time/residue: 0.5567 time to fit residues: 55.9184 Evaluate side-chains 87 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1220 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119693 restraints weight = 12819.448| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.37 r_work: 0.3295 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9910 Z= 0.109 Angle : 0.532 8.328 13592 Z= 0.278 Chirality : 0.037 0.197 1506 Planarity : 0.003 0.046 1548 Dihedral : 16.320 178.179 1803 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.31 % Allowed : 29.86 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.28), residues: 1007 helix: 2.54 (0.20), residues: 662 sheet: -1.19 (0.96), residues: 30 loop : -2.31 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 949 TYR 0.013 0.001 TYR A 910 PHE 0.010 0.001 PHE A 909 TRP 0.019 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 9910) covalent geometry : angle 0.53218 / 0.28 (13592) hydrogen bonds : bond 0.05272 / 3.77 ( 497) hydrogen bonds : angle 3.11549 / 2.23 ( 1433) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5356 (OUTLIER) cc_final: 0.4997 (pmm150) REVERT: A 441 GLU cc_start: 0.7866 (mp0) cc_final: 0.7614 (mp0) REVERT: A 445 LYS cc_start: 0.8463 (tmtm) cc_final: 0.8245 (tmmm) REVERT: A 556 ASP cc_start: 0.7746 (p0) cc_final: 0.7511 (p0) REVERT: A 732 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7534 (ttpt) REVERT: A 830 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6224 (pm20) REVERT: A 977 CYS cc_start: 0.7252 (m) cc_final: 0.7014 (m) REVERT: A 1106 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7841 (tppt) REVERT: A 1220 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8521 (mmp) outliers start: 21 outliers final: 7 residues processed: 96 average time/residue: 0.5830 time to fit residues: 59.4097 Evaluate side-chains 87 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1220 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117074 restraints weight = 12769.089| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.33 r_work: 0.3255 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9910 Z= 0.141 Angle : 0.563 8.444 13592 Z= 0.293 Chirality : 0.039 0.247 1506 Planarity : 0.003 0.040 1548 Dihedral : 16.369 177.254 1803 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.63 % Allowed : 29.86 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.27), residues: 1007 helix: 2.50 (0.20), residues: 663 sheet: -1.20 (0.96), residues: 30 loop : -2.33 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 949 TYR 0.013 0.001 TYR A 344 PHE 0.015 0.001 PHE A 909 TRP 0.018 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9910) covalent geometry : angle 0.56325 / 0.29 (13592) hydrogen bonds : bond 0.05822 / 4.09 ( 497) hydrogen bonds : angle 3.17545 / 2.26 ( 1433) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5372 (OUTLIER) cc_final: 0.4974 (pmm150) REVERT: A 445 LYS cc_start: 0.8477 (tmtm) cc_final: 0.8256 (tmmm) REVERT: A 556 ASP cc_start: 0.7778 (p0) cc_final: 0.7526 (p0) REVERT: A 732 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7625 (ttpt) REVERT: A 746 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7341 (ttt-90) REVERT: A 830 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6233 (pm20) REVERT: A 977 CYS cc_start: 0.7196 (m) cc_final: 0.6957 (m) REVERT: A 1214 ASP cc_start: 0.8120 (m-30) cc_final: 0.7907 (m-30) outliers start: 24 outliers final: 11 residues processed: 97 average time/residue: 0.5608 time to fit residues: 58.0211 Evaluate side-chains 87 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.160215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119687 restraints weight = 12750.604| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.37 r_work: 0.3291 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9910 Z= 0.116 Angle : 0.550 8.714 13592 Z= 0.285 Chirality : 0.038 0.198 1506 Planarity : 0.003 0.039 1548 Dihedral : 16.302 178.037 1803 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.41 % Allowed : 30.41 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.28), residues: 1007 helix: 2.62 (0.20), residues: 661 sheet: -1.15 (0.96), residues: 30 loop : -2.28 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 949 TYR 0.016 0.001 TYR A 843 PHE 0.011 0.001 PHE A 909 TRP 0.020 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 9910) covalent geometry : angle 0.54967 / 0.29 (13592) hydrogen bonds : bond 0.05286 / 3.77 ( 497) hydrogen bonds : angle 3.08907 / 2.21 ( 1433) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5471 (OUTLIER) cc_final: 0.5089 (pmm150) REVERT: A 441 GLU cc_start: 0.7871 (mp0) cc_final: 0.7616 (mp0) REVERT: A 445 LYS cc_start: 0.8476 (tmtm) cc_final: 0.8261 (tmmm) REVERT: A 556 ASP cc_start: 0.7691 (p0) cc_final: 0.7450 (p0) REVERT: A 732 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7467 (ttmt) REVERT: A 830 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: A 977 CYS cc_start: 0.7291 (m) cc_final: 0.7059 (m) REVERT: A 1214 ASP cc_start: 0.8148 (m-30) cc_final: 0.7942 (m-30) REVERT: A 1220 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8521 (mmp) outliers start: 22 outliers final: 11 residues processed: 96 average time/residue: 0.5645 time to fit residues: 57.8071 Evaluate side-chains 88 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1220 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.160224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119646 restraints weight = 12753.417| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.36 r_work: 0.3285 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9910 Z= 0.116 Angle : 0.552 8.856 13592 Z= 0.286 Chirality : 0.038 0.228 1506 Planarity : 0.003 0.040 1548 Dihedral : 16.277 178.296 1803 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 2.20 % Allowed : 30.63 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.28), residues: 1007 helix: 2.68 (0.20), residues: 663 sheet: -1.13 (0.96), residues: 30 loop : -2.28 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 949 TYR 0.020 0.001 TYR A 843 PHE 0.011 0.001 PHE A 909 TRP 0.019 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9910) covalent geometry : angle 0.55168 / 0.29 (13592) hydrogen bonds : bond 0.05336 / 3.82 ( 497) hydrogen bonds : angle 3.06731 / 2.19 ( 1433) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5419 (OUTLIER) cc_final: 0.5045 (pmm150) REVERT: A 407 ILE cc_start: 0.7750 (mt) cc_final: 0.7541 (mm) REVERT: A 441 GLU cc_start: 0.7882 (mp0) cc_final: 0.7611 (mp0) REVERT: A 445 LYS cc_start: 0.8452 (tmtm) cc_final: 0.8239 (tmmm) REVERT: A 556 ASP cc_start: 0.7650 (p0) cc_final: 0.7425 (p0) REVERT: A 732 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7468 (ttmt) REVERT: A 830 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: A 977 CYS cc_start: 0.7290 (m) cc_final: 0.7040 (m) REVERT: A 1214 ASP cc_start: 0.8146 (m-30) cc_final: 0.7930 (m-30) outliers start: 20 outliers final: 11 residues processed: 95 average time/residue: 0.5284 time to fit residues: 53.6540 Evaluate side-chains 89 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118933 restraints weight = 12656.797| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.35 r_work: 0.3275 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9910 Z= 0.126 Angle : 0.568 9.003 13592 Z= 0.294 Chirality : 0.038 0.221 1506 Planarity : 0.003 0.045 1548 Dihedral : 16.280 177.987 1803 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.41 % Allowed : 30.41 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.27), residues: 1007 helix: 2.66 (0.20), residues: 663 sheet: -1.12 (0.96), residues: 30 loop : -2.30 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 992 TYR 0.023 0.001 TYR A 843 PHE 0.010 0.001 PHE A 909 TRP 0.020 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9910) covalent geometry : angle 0.56788 / 0.29 (13592) hydrogen bonds : bond 0.05496 / 3.91 ( 497) hydrogen bonds : angle 3.09940 / 2.22 ( 1433) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.5085 (pmm150) REVERT: A 407 ILE cc_start: 0.7772 (mt) cc_final: 0.7563 (mm) REVERT: A 441 GLU cc_start: 0.7879 (mp0) cc_final: 0.7666 (mp0) REVERT: A 445 LYS cc_start: 0.8415 (tmtm) cc_final: 0.8202 (tmmm) REVERT: A 556 ASP cc_start: 0.7634 (p0) cc_final: 0.7421 (p0) REVERT: A 732 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7515 (ttmt) REVERT: A 830 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6240 (pm20) REVERT: A 900 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: A 977 CYS cc_start: 0.7243 (m) cc_final: 0.7001 (m) REVERT: A 1214 ASP cc_start: 0.8150 (m-30) cc_final: 0.7929 (m-30) outliers start: 22 outliers final: 11 residues processed: 94 average time/residue: 0.4840 time to fit residues: 48.6527 Evaluate side-chains 88 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118702 restraints weight = 12673.779| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.36 r_work: 0.3273 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9910 Z= 0.127 Angle : 0.575 9.110 13592 Z= 0.298 Chirality : 0.039 0.218 1506 Planarity : 0.003 0.051 1548 Dihedral : 16.263 177.797 1803 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.98 % Allowed : 31.06 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.27), residues: 1007 helix: 2.64 (0.20), residues: 663 sheet: -1.15 (0.96), residues: 30 loop : -2.33 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 949 TYR 0.027 0.001 TYR A 843 PHE 0.011 0.001 PHE A 909 TRP 0.021 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9910) covalent geometry : angle 0.57484 / 0.30 (13592) hydrogen bonds : bond 0.05359 / 3.79 ( 497) hydrogen bonds : angle 3.11239 / 2.23 ( 1433) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.5046 (pmm150) REVERT: A 407 ILE cc_start: 0.7777 (mt) cc_final: 0.7573 (mm) REVERT: A 441 GLU cc_start: 0.7867 (mp0) cc_final: 0.7649 (mp0) REVERT: A 445 LYS cc_start: 0.8426 (tmtm) cc_final: 0.8216 (tmmm) REVERT: A 556 ASP cc_start: 0.7634 (p0) cc_final: 0.7428 (p0) REVERT: A 732 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7530 (ttmt) REVERT: A 830 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6275 (pm20) REVERT: A 977 CYS cc_start: 0.7252 (m) cc_final: 0.7013 (m) REVERT: A 1214 ASP cc_start: 0.8149 (m-30) cc_final: 0.7944 (m-30) outliers start: 18 outliers final: 12 residues processed: 91 average time/residue: 0.5002 time to fit residues: 48.9202 Evaluate side-chains 87 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114271 restraints weight = 12656.120| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.36 r_work: 0.3199 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9910 Z= 0.202 Angle : 0.644 9.155 13592 Z= 0.334 Chirality : 0.043 0.294 1506 Planarity : 0.004 0.051 1548 Dihedral : 16.410 176.117 1803 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.09 % Allowed : 30.63 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.27), residues: 1007 helix: 2.36 (0.20), residues: 664 sheet: -1.40 (0.94), residues: 30 loop : -2.47 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 949 TYR 0.026 0.002 TYR A 843 PHE 0.016 0.002 PHE A 909 TRP 0.027 0.002 TRP A 887 HIS 0.005 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 9910) covalent geometry : angle 0.64449 / 0.33 (13592) hydrogen bonds : bond 0.06411 / 4.42 ( 497) hydrogen bonds : angle 3.33468 / 2.38 ( 1433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.36 seconds wall clock time: 37 minutes 57.88 seconds (2277.88 seconds total)