Starting phenix.real_space_refine on Wed Aug 5 11:52:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ewg_28645/08_2026/8ewg_28645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ewg_28645/08_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_28645/08_2026/8ewg_28645.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ewg_28645/08_2026/8ewg_28645.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ewg_28645/08_2026/8ewg_28645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ewg_28645/08_2026/8ewg_28645.map" model { file = "/net/cci-nas-00/data/ceres_data/8ewg_28645/08_2026/8ewg_28645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ewg_28645/08_2026/8ewg_28645.cif" } 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-2.2rc3-6140/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 Classifications: {'RNAv2': 56} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 34} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.86, per 1000 atoms: 0.19 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: 0.88 Conformation dependent library (CDL) restraints added in 273.1 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: 1.22 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: 1.92 Time building geometry restraints manager: 1.15 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=" 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 bond pdb=" CG ARG A 949 " pdb=" CD ARG A 949 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.96e+00 ... (remaining 9905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 13084 2.28 - 4.55: 425 4.55 - 6.83: 68 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=" C3' G B 2 " pdb=" O3' G B 2 " pdb=" P G B 3 " ideal model delta sigma weight residual 119.70 123.87 -4.17 1.20e+00 6.94e-01 1.21e+01 ... (remaining 13587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.21: 5175 26.21 - 52.42: 585 52.42 - 78.63: 170 78.63 - 104.85: 13 104.85 - 131.06: 1 Dihedral angle restraints: 5944 sinusoidal: 2948 harmonic: 2996 Sorted by residual: dihedral pdb=" C4' U B 42 " pdb=" C3' U B 42 " pdb=" C2' U B 42 " pdb=" C1' U B 42 " ideal model delta sinusoidal sigma weight residual 36.34 -39.15 75.50 1 3.10e+00 1.04e-01 7.49e+02 dihedral pdb=" C4' A B 27 " pdb=" C3' A B 27 " pdb=" C2' A B 27 " pdb=" C1' A B 27 " ideal model delta sinusoidal sigma weight residual 36.35 -38.45 74.80 1 3.10e+00 1.04e-01 7.37e+02 dihedral pdb=" C4' A B 52 " pdb=" C3' A B 52 " pdb=" C2' A B 52 " pdb=" C1' A B 52 " ideal model delta sinusoidal sigma weight residual 36.34 -38.41 74.76 1 3.10e+00 1.04e-01 7.36e+02 ... (remaining 5941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1253 0.072 - 0.144: 133 0.144 - 0.216: 36 0.216 - 0.288: 70 0.288 - 0.361: 14 Chirality restraints: 1506 Sorted by residual: chirality pdb=" P A B 8 " pdb=" OP1 A B 8 " pdb=" OP2 A B 8 " pdb=" O5' A B 8 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" P G B 3 " pdb=" OP1 G B 3 " pdb=" OP2 G B 3 " pdb=" O5' G B 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.85e+00 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 ... (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: 0.790 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.640 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: 0.010 Load rotamer database and sin/cos tables:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- 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= 0.210 Angle : 0.919 11.377 13592 Z= 0.452 Chirality : 0.079 0.361 1506 Planarity : 0.006 0.090 1548 Dihedral : 21.987 131.057 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 0.00439 / 0.21 ( 9910) covalent geometry : angle 0.91945 / 0.45 (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 : 0.323 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: 0.6481 time to fit residues: 64.2142 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 : 0.266 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121435 restraints weight = 12726.928| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.30 r_work: 0.3315 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9910 Z= 0.175 Angle : 1.011 26.521 13592 Z= 0.429 Chirality : 0.101 1.163 1506 Planarity : 0.004 0.074 1548 Dihedral : 15.842 158.404 1807 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.29 % Allowed : 27.66 % Favored : 69.05 % 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: 0.45 (0.27), residues: 1007 helix: 1.60 (0.20), residues: 668 sheet: -1.50 (1.09), residues: 20 loop : -2.54 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 949 TYR 0.012 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 0.00364 / 0.17 ( 9910) covalent geometry : angle 1.01129 / 0.43 (13592) hydrogen bonds : bond 0.07202 / 5.19 ( 497) hydrogen bonds : angle 3.52265 / 2.49 ( 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: 30 poor density : 88 time to evaluate : 0.345 Fit side-chains REVERT: A 445 LYS cc_start: 0.8464 (tmtm) cc_final: 0.8263 (tmmm) REVERT: A 732 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7452 (ttmt) REVERT: A 733 GLN cc_start: 0.8087 (mt0) cc_final: 0.7809 (mt0) REVERT: A 830 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6385 (pm20) REVERT: A 977 CYS cc_start: 0.7139 (m) cc_final: 0.6856 (m) outliers start: 30 outliers final: 7 residues processed: 107 average time/residue: 0.6062 time to fit residues: 68.9194 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 : 0.309 ------------------------------------------------------------------------------- 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: 0.9980 chunk 65 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 HIS A 838 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125530 restraints weight = 12708.137| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.28 r_work: 0.3380 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9910 Z= 0.133 Angle : 0.815 18.840 13592 Z= 0.351 Chirality : 0.071 0.815 1506 Planarity : 0.003 0.059 1548 Dihedral : 15.328 176.312 1803 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.85 % Allowed : 28.54 % Favored : 68.61 % 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: 2.16 (0.20), residues: 662 sheet: -1.42 (1.09), residues: 20 loop : -2.39 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 949 TYR 0.009 0.001 TYR A 910 PHE 0.009 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 0.00275 / 0.13 ( 9910) covalent geometry : angle 0.81482 / 0.35 (13592) hydrogen bonds : bond 0.05705 / 4.14 ( 497) hydrogen bonds : angle 3.22049 / 2.30 ( 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 112 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 718 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: A 732 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7532 (ttpt) REVERT: A 733 GLN cc_start: 0.8018 (mt0) cc_final: 0.7813 (mt0) REVERT: A 752 LYS cc_start: 0.7096 (mptp) cc_final: 0.6684 (mptp) REVERT: A 830 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6237 (pm20) REVERT: A 977 CYS cc_start: 0.7191 (m) cc_final: 0.6931 (m) REVERT: A 1214 ASP cc_start: 0.8128 (m-30) cc_final: 0.7853 (m-30) outliers start: 26 outliers final: 5 residues processed: 105 average time/residue: 0.5680 time to fit residues: 63.6661 Evaluate side-chains 79 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 430 LYS 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 Chi-restraints excluded: chain A residue 1154 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1058 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.162037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121854 restraints weight = 12896.040| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.34 r_work: 0.3328 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9910 Z= 0.141 Angle : 0.805 18.038 13592 Z= 0.347 Chirality : 0.069 0.779 1506 Planarity : 0.003 0.051 1548 Dihedral : 15.157 164.825 1803 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.41 % Allowed : 29.86 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.33 (0.28), residues: 1007 helix: 2.38 (0.20), residues: 661 sheet: -1.16 (0.95), residues: 30 loop : -2.37 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 949 TYR 0.012 0.001 TYR A 344 PHE 0.013 0.001 PHE A 909 TRP 0.015 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 9910) covalent geometry : angle 0.80517 / 0.35 (13592) hydrogen bonds : bond 0.05450 / 3.84 ( 497) hydrogen bonds : angle 3.16525 / 2.25 ( 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: 22 poor density : 81 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.7904 (mp0) cc_final: 0.7675 (mp0) REVERT: A 732 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7588 (ttpt) REVERT: A 830 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6215 (pm20) REVERT: A 900 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: A 977 CYS cc_start: 0.7254 (m) cc_final: 0.6993 (m) REVERT: A 1181 MET cc_start: 0.7822 (mmm) cc_final: 0.7520 (mpp) REVERT: A 1214 ASP cc_start: 0.8112 (m-30) cc_final: 0.7857 (m-30) outliers start: 22 outliers final: 7 residues processed: 96 average time/residue: 0.6137 time to fit residues: 62.6983 Evaluate side-chains 84 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 700 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 900 GLU Chi-restraints excluded: chain A residue 1200 LEU 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: 5.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.161847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121626 restraints weight = 12905.396| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.36 r_work: 0.3328 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2388 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= 0.139 Angle : 0.782 17.151 13592 Z= 0.339 Chirality : 0.068 0.895 1506 Planarity : 0.003 0.048 1548 Dihedral : 15.264 169.521 1803 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.07 % Allowed : 28.98 % Favored : 67.95 % 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: 1.44 (0.27), residues: 1007 helix: 2.46 (0.20), residues: 665 sheet: -1.49 (1.10), residues: 20 loop : -2.31 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 746 TYR 0.015 0.001 TYR A 843 PHE 0.010 0.001 PHE A 909 TRP 0.016 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 9910) covalent geometry : angle 0.78191 / 0.34 (13592) hydrogen bonds : bond 0.05397 / 3.80 ( 497) hydrogen bonds : angle 3.15154 / 2.25 ( 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 108 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.7901 (mp0) cc_final: 0.7643 (mp0) REVERT: A 699 GLN cc_start: 0.7697 (mm110) cc_final: 0.7488 (mm-40) REVERT: A 732 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7616 (ttpt) REVERT: A 830 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6274 (pm20) REVERT: A 977 CYS cc_start: 0.7226 (m) cc_final: 0.6971 (m) REVERT: A 1181 MET cc_start: 0.7818 (mmm) cc_final: 0.7555 (mpp) REVERT: A 1214 ASP cc_start: 0.8115 (m-30) cc_final: 0.7886 (m-30) outliers start: 28 outliers final: 8 residues processed: 99 average time/residue: 0.5921 time to fit residues: 62.3212 Evaluate side-chains 85 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ARG 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 506 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 1154 MET Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 750 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123224 restraints weight = 12917.245| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.34 r_work: 0.3349 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9910 Z= 0.126 Angle : 0.758 16.740 13592 Z= 0.329 Chirality : 0.065 0.822 1506 Planarity : 0.003 0.042 1548 Dihedral : 15.351 172.529 1803 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.31 % Allowed : 29.75 % Favored : 67.95 % 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: 1.56 (0.28), residues: 1007 helix: 2.58 (0.20), residues: 664 sheet: -1.14 (0.95), residues: 30 loop : -2.36 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 949 TYR 0.014 0.001 TYR A 843 PHE 0.010 0.001 PHE A 909 TRP 0.019 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 9910) covalent geometry : angle 0.75773 / 0.33 (13592) hydrogen bonds : bond 0.05076 / 3.61 ( 497) hydrogen bonds : angle 3.08470 / 2.21 ( 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 105 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.4995 (pmm150) REVERT: A 441 GLU cc_start: 0.7884 (mp0) cc_final: 0.7634 (mp0) REVERT: A 732 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7490 (ttpt) REVERT: A 830 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6237 (pm20) REVERT: A 977 CYS cc_start: 0.7296 (m) cc_final: 0.7037 (m) REVERT: A 1214 ASP cc_start: 0.8118 (m-30) cc_final: 0.7857 (m-30) outliers start: 21 outliers final: 8 residues processed: 99 average time/residue: 0.5765 time to fit residues: 60.7819 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 : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 275 ARG 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 1154 MET 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: 5.9990 chunk 3 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 ASN A 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116006 restraints weight = 12943.319| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.35 r_work: 0.3236 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9910 Z= 0.216 Angle : 0.889 16.807 13592 Z= 0.391 Chirality : 0.079 0.869 1506 Planarity : 0.004 0.061 1548 Dihedral : 15.579 173.935 1803 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.52 % Allowed : 30.19 % 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: 1.19 (0.27), residues: 1007 helix: 2.29 (0.20), residues: 665 sheet: -1.30 (0.92), residues: 30 loop : -2.51 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 949 TYR 0.019 0.002 TYR A 344 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 0.00498 / 0.22 ( 9910) covalent geometry : angle 0.88944 / 0.39 (13592) hydrogen bonds : bond 0.06598 / 4.55 ( 497) hydrogen bonds : angle 3.35029 / 2.38 ( 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 104 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.5040 (pmm150) REVERT: A 405 ASN cc_start: 0.8017 (t0) cc_final: 0.7789 (t0) REVERT: A 556 ASP cc_start: 0.7897 (p0) cc_final: 0.7634 (p0) REVERT: A 732 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7657 (ttpt) REVERT: A 830 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6458 (pm20) REVERT: A 977 CYS cc_start: 0.7230 (m) cc_final: 0.6987 (m) REVERT: A 1214 ASP cc_start: 0.8152 (m-30) cc_final: 0.7916 (m-30) outliers start: 23 outliers final: 11 residues processed: 101 average time/residue: 0.5608 time to fit residues: 60.4152 Evaluate side-chains 85 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG 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 506 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1200 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.162127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122696 restraints weight = 12899.636| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.33 r_work: 0.3343 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2693 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 : 0.777 17.836 13592 Z= 0.340 Chirality : 0.065 0.694 1506 Planarity : 0.003 0.038 1548 Dihedral : 15.516 175.195 1803 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.63 % Allowed : 30.08 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.27), residues: 1007 helix: 2.56 (0.20), residues: 663 sheet: -1.20 (0.92), residues: 30 loop : -2.37 (0.32), 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 0.008 0.001 PHE A1174 TRP 0.023 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9910) covalent geometry : angle 0.77657 / 0.34 (13592) hydrogen bonds : bond 0.04983 / 3.55 ( 497) hydrogen bonds : angle 3.13622 / 2.24 ( 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 104 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.5079 (pmm150) REVERT: A 405 ASN cc_start: 0.7936 (t0) cc_final: 0.7724 (t0) REVERT: A 732 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7414 (ttmt) REVERT: A 830 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6272 (pm20) REVERT: A 838 GLN cc_start: 0.7886 (tp40) cc_final: 0.7631 (tp40) REVERT: A 977 CYS cc_start: 0.7329 (m) cc_final: 0.7092 (m) REVERT: A 1214 ASP cc_start: 0.8109 (m-30) cc_final: 0.7865 (m-30) outliers start: 24 outliers final: 12 residues processed: 96 average time/residue: 0.5515 time to fit residues: 56.6415 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 : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 275 ARG 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 551 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 884 GLU 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: 0.7980 chunk 92 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.163231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123896 restraints weight = 12833.003| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.33 r_work: 0.3363 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9910 Z= 0.124 Angle : 0.767 17.168 13592 Z= 0.337 Chirality : 0.063 0.680 1506 Planarity : 0.003 0.041 1548 Dihedral : 15.434 176.045 1803 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.41 % Allowed : 30.30 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.65 (0.27), residues: 1007 helix: 2.66 (0.20), residues: 663 sheet: -1.11 (0.93), residues: 30 loop : -2.37 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 949 TYR 0.023 0.001 TYR A 843 PHE 0.009 0.001 PHE A 909 TRP 0.024 0.002 TRP A 269 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9910) covalent geometry : angle 0.76707 / 0.34 (13592) hydrogen bonds : bond 0.04798 / 3.41 ( 497) hydrogen bonds : angle 3.08060 / 2.21 ( 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 101 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5498 (OUTLIER) cc_final: 0.5111 (pmm150) REVERT: A 732 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7444 (ttmt) REVERT: A 830 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5998 (pm20) REVERT: A 838 GLN cc_start: 0.7879 (tp40) cc_final: 0.7597 (tp40) REVERT: A 900 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 904 LYS cc_start: 0.8610 (tppt) cc_final: 0.8266 (mmmt) REVERT: A 977 CYS cc_start: 0.7233 (m) cc_final: 0.6980 (m) REVERT: A 1214 ASP cc_start: 0.8121 (m-30) cc_final: 0.7820 (m-30) outliers start: 22 outliers final: 10 residues processed: 97 average time/residue: 0.5212 time to fit residues: 54.1637 Evaluate side-chains 85 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 275 ARG 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 551 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 753 THR 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 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: 5.9990 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.4998 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.160202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120260 restraints weight = 12867.211| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.34 r_work: 0.3306 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9910 Z= 0.152 Angle : 0.816 17.113 13592 Z= 0.359 Chirality : 0.068 0.673 1506 Planarity : 0.004 0.044 1548 Dihedral : 15.520 177.069 1803 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.87 % Allowed : 31.06 % Favored : 67.07 % 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: 1.51 (0.27), residues: 1007 helix: 2.54 (0.20), residues: 664 sheet: -1.21 (0.93), residues: 30 loop : -2.40 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 949 TYR 0.029 0.002 TYR A 843 PHE 0.011 0.001 PHE A 909 TRP 0.037 0.002 TRP A 269 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9910) covalent geometry : angle 0.81558 / 0.36 (13592) hydrogen bonds : bond 0.05371 / 3.76 ( 497) hydrogen bonds : angle 3.17739 / 2.26 ( 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: 17 poor density : 76 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5447 (OUTLIER) cc_final: 0.5085 (pmm150) REVERT: A 732 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7560 (ttmt) REVERT: A 830 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6284 (pm20) REVERT: A 838 GLN cc_start: 0.7888 (tp40) cc_final: 0.7592 (tp40) REVERT: A 900 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: A 977 CYS cc_start: 0.7225 (m) cc_final: 0.6973 (m) REVERT: A 1214 ASP cc_start: 0.8146 (m-30) cc_final: 0.7934 (m-30) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.5302 time to fit residues: 51.4963 Evaluate side-chains 86 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 275 ARG 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 551 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 753 THR 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 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: 0.0060 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.163090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123466 restraints weight = 12898.153| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.35 r_work: 0.3346 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9910 Z= 0.131 Angle : 0.790 17.091 13592 Z= 0.349 Chirality : 0.064 0.588 1506 Planarity : 0.003 0.045 1548 Dihedral : 15.474 177.400 1803 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 1.87 % Allowed : 30.95 % 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: 1.60 (0.27), residues: 1007 helix: 2.62 (0.20), residues: 663 sheet: -1.21 (0.95), residues: 30 loop : -2.36 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 949 TYR 0.029 0.001 TYR A 843 PHE 0.009 0.001 PHE A 909 TRP 0.037 0.002 TRP A 269 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9910) covalent geometry : angle 0.78950 / 0.35 (13592) hydrogen bonds : bond 0.04762 / 3.38 ( 497) hydrogen bonds : angle 3.11155 / 2.23 ( 1433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2310.81 seconds wall clock time: 40 minutes 12.32 seconds (2412.32 seconds total)