Starting phenix.real_space_refine on Wed Mar 4 01:03:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ewg_28645/03_2026/8ewg_28645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ewg_28645/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ewg_28645/03_2026/8ewg_28645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ewg_28645/03_2026/8ewg_28645.map" model { file = "/net/cci-nas-00/data/ceres_data/8ewg_28645/03_2026/8ewg_28645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ewg_28645/03_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-dev-5986/lib/python3.9/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: 2.27, per 1000 atoms: 0.24 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: 0.72 Conformation dependent library (CDL) restraints added in 376.7 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: 1.12 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: 1.61 Time building geometry restraints manager: 0.96 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: 5708 35.69 - 71.38: 383 71.38 - 107.07: 46 107.07 - 142.76: 1 142.76 - 178.45: 6 Dihedral angle restraints: 6144 sinusoidal: 3148 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 6141 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: 0.640 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.590 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 22.251 178.449 4202 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 covalent geometry : bond 0.00425 ( 9910) covalent geometry : angle 0.81046 (13592) hydrogen bonds : bond 0.15338 ( 497) hydrogen bonds : angle 4.98969 ( 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 : 0.282 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: 0.6003 time to fit residues: 59.6284 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 : 0.318 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 361 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 = 0.3950 r_free = 0.3950 target = 0.159773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119948 restraints weight = 12757.364| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.33 r_work: 0.3285 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1116 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= 0.139 Angle : 0.578 6.401 13592 Z= 0.305 Chirality : 0.040 0.226 1506 Planarity : 0.004 0.074 1548 Dihedral : 20.321 177.947 2007 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.51 % Allowed : 27.22 % 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: 0.51 (0.27), residues: 1007 helix: 1.67 (0.20), residues: 664 sheet: -1.54 (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 0.012 0.001 TYR A 344 PHE 0.017 0.001 PHE A 909 TRP 0.017 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9910) covalent geometry : angle 0.57829 (13592) hydrogen bonds : bond 0.06449 ( 497) hydrogen bonds : angle 3.47338 ( 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 121 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.283 Fit side-chains REVERT: A 445 LYS cc_start: 0.8512 (tmtm) cc_final: 0.8312 (tmmm) REVERT: A 732 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7472 (ttmt) REVERT: A 733 GLN cc_start: 0.8085 (mt0) cc_final: 0.7766 (mt0) REVERT: A 830 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6282 (pm20) REVERT: A 977 CYS cc_start: 0.7119 (m) cc_final: 0.6873 (m) outliers start: 32 outliers final: 7 residues processed: 110 average time/residue: 0.6484 time to fit residues: 75.8093 Evaluate side-chains 82 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3983 r_free = 0.3983 target = 0.162737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123044 restraints weight = 12709.251| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.31 r_work: 0.3338 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9910 Z= 0.105 Angle : 0.530 6.644 13592 Z= 0.276 Chirality : 0.037 0.198 1506 Planarity : 0.003 0.061 1548 Dihedral : 20.066 179.660 2003 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.85 % Allowed : 28.87 % Favored : 68.28 % 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: 1.14 (0.27), residues: 1007 helix: 2.23 (0.20), residues: 659 sheet: -1.43 (1.11), residues: 20 loop : -2.36 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 949 TYR 0.010 0.001 TYR A 910 PHE 0.009 0.001 PHE A 909 TRP 0.015 0.001 TRP A 887 HIS 0.003 0.000 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9910) covalent geometry : angle 0.52954 (13592) hydrogen bonds : bond 0.05224 ( 497) hydrogen bonds : angle 3.20600 ( 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: 26 poor density : 83 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.8498 (tmtm) cc_final: 0.8297 (tmmm) REVERT: A 732 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7474 (ttmt) REVERT: A 733 GLN cc_start: 0.8042 (mt0) cc_final: 0.7818 (mt0) REVERT: A 830 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6194 (pm20) REVERT: A 1214 ASP cc_start: 0.8100 (m-30) cc_final: 0.7834 (m-30) outliers start: 26 outliers final: 3 residues processed: 102 average time/residue: 0.6169 time to fit residues: 67.1774 Evaluate side-chains 78 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9990 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.161585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121190 restraints weight = 12875.401| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.37 r_work: 0.3311 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9910 Z= 0.112 Angle : 0.539 8.140 13592 Z= 0.277 Chirality : 0.038 0.196 1506 Planarity : 0.003 0.052 1548 Dihedral : 20.007 178.934 2003 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.20 % Allowed : 29.75 % 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: 1.43 (0.28), residues: 1007 helix: 2.45 (0.20), residues: 663 sheet: -1.49 (1.10), residues: 20 loop : -2.31 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 949 TYR 0.011 0.001 TYR A 843 PHE 0.011 0.001 PHE A 909 TRP 0.017 0.001 TRP A 887 HIS 0.003 0.001 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9910) covalent geometry : angle 0.53853 (13592) hydrogen bonds : bond 0.05548 ( 497) hydrogen bonds : angle 3.09901 ( 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 99 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.7903 (mp0) cc_final: 0.7665 (mp0) REVERT: A 445 LYS cc_start: 0.8472 (tmtm) cc_final: 0.8265 (tmmm) REVERT: A 732 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7540 (ttpt) REVERT: A 733 GLN cc_start: 0.8086 (mt0) cc_final: 0.7830 (mt0) REVERT: A 830 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6229 (pm20) REVERT: A 900 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: A 977 CYS cc_start: 0.7287 (m) cc_final: 0.7024 (m) REVERT: A 1214 ASP cc_start: 0.8142 (m-30) cc_final: 0.7917 (m-30) outliers start: 20 outliers final: 6 residues processed: 94 average time/residue: 0.6808 time to fit residues: 68.0390 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 : 0.367 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.159458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118716 restraints weight = 12783.071| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.36 r_work: 0.3278 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1821 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= 0.131 Angle : 0.551 7.680 13592 Z= 0.288 Chirality : 0.039 0.230 1506 Planarity : 0.003 0.046 1548 Dihedral : 20.011 177.771 2003 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 2.74 % Allowed : 28.98 % Favored : 68.28 % 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: 1.50 (0.28), residues: 1007 helix: 2.53 (0.20), residues: 663 sheet: -1.18 (0.96), residues: 30 loop : -2.37 (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 843 PHE 0.012 0.001 PHE A 909 TRP 0.019 0.001 TRP A 887 HIS 0.003 0.001 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9910) covalent geometry : angle 0.55109 (13592) hydrogen bonds : bond 0.05731 ( 497) hydrogen bonds : angle 3.12749 ( 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 102 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.7872 (mp0) cc_final: 0.7620 (mp0) REVERT: A 445 LYS cc_start: 0.8479 (tmtm) cc_final: 0.8271 (tmmm) REVERT: A 732 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7643 (ttpt) REVERT: A 830 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6270 (pm20) REVERT: A 977 CYS cc_start: 0.7237 (m) cc_final: 0.6984 (m) REVERT: A 1214 ASP cc_start: 0.8134 (m-30) cc_final: 0.7910 (m-30) outliers start: 25 outliers final: 6 residues processed: 95 average time/residue: 0.6772 time to fit residues: 68.3949 Evaluate side-chains 80 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115240 restraints weight = 12802.349| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.38 r_work: 0.3225 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9910 Z= 0.174 Angle : 0.603 8.211 13592 Z= 0.313 Chirality : 0.041 0.283 1506 Planarity : 0.004 0.045 1548 Dihedral : 20.140 176.051 2003 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.96 % Allowed : 29.31 % Favored : 67.73 % 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: 1.29 (0.27), residues: 1007 helix: 2.37 (0.20), residues: 663 sheet: -1.41 (0.93), residues: 30 loop : -2.45 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 949 TYR 0.016 0.002 TYR A 344 PHE 0.014 0.001 PHE A 909 TRP 0.026 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9910) covalent geometry : angle 0.60286 (13592) hydrogen bonds : bond 0.06323 ( 497) hydrogen bonds : angle 3.28841 ( 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 104 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.5053 (pmm150) REVERT: A 732 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7733 (ttpt) REVERT: A 830 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6413 (pm20) REVERT: A 977 CYS cc_start: 0.7227 (m) cc_final: 0.6984 (m) REVERT: A 1199 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7438 (ptm160) REVERT: A 1200 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6812 (mp) REVERT: A 1214 ASP cc_start: 0.8152 (m-30) cc_final: 0.7923 (m-30) outliers start: 27 outliers final: 8 residues processed: 96 average time/residue: 0.6945 time to fit residues: 70.9417 Evaluate side-chains 87 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 830 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 1199 ARG 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: 0.5980 chunk 3 optimal weight: 0.0770 chunk 60 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.161239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121136 restraints weight = 12757.384| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.34 r_work: 0.3310 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9910 Z= 0.110 Angle : 0.551 8.782 13592 Z= 0.286 Chirality : 0.038 0.198 1506 Planarity : 0.003 0.042 1548 Dihedral : 20.022 178.167 2003 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.41 % Allowed : 30.08 % 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: 1.62 (0.27), residues: 1007 helix: 2.66 (0.20), residues: 659 sheet: -1.19 (0.94), residues: 30 loop : -2.35 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 949 TYR 0.018 0.001 TYR A 843 PHE 0.007 0.001 PHE A1212 TRP 0.025 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9910) covalent geometry : angle 0.55067 (13592) hydrogen bonds : bond 0.04911 ( 497) hydrogen bonds : angle 3.07777 ( 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 103 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.5089 (pmm150) REVERT: A 427 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: A 445 LYS cc_start: 0.8470 (tmtm) cc_final: 0.8266 (tmmm) REVERT: A 732 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7560 (ttpt) REVERT: A 830 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6249 (pm20) REVERT: A 900 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: A 977 CYS cc_start: 0.7301 (m) cc_final: 0.7045 (m) REVERT: A 1214 ASP cc_start: 0.8130 (m-30) cc_final: 0.7917 (m-30) outliers start: 22 outliers final: 5 residues processed: 98 average time/residue: 0.7093 time to fit residues: 73.4332 Evaluate side-chains 83 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 427 GLU 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 900 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.158862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118382 restraints weight = 12769.759| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.33 r_work: 0.3276 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2098 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= 0.135 Angle : 0.578 8.806 13592 Z= 0.299 Chirality : 0.039 0.225 1506 Planarity : 0.003 0.041 1548 Dihedral : 20.023 177.803 2003 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.20 % Allowed : 30.41 % Favored : 67.40 % 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: 2.63 (0.20), residues: 664 sheet: -1.22 (0.96), residues: 30 loop : -2.40 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 949 TYR 0.022 0.001 TYR A 843 PHE 0.011 0.001 PHE A 909 TRP 0.024 0.001 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9910) covalent geometry : angle 0.57842 (13592) hydrogen bonds : bond 0.05620 ( 497) hydrogen bonds : angle 3.13403 ( 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 95 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5443 (OUTLIER) cc_final: 0.5068 (pmm150) REVERT: A 445 LYS cc_start: 0.8436 (tmtm) cc_final: 0.8209 (tmmm) REVERT: A 732 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7631 (ttpt) REVERT: A 830 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6277 (pm20) REVERT: A 900 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: A 977 CYS cc_start: 0.7292 (m) cc_final: 0.7040 (m) REVERT: A 1200 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6844 (mp) REVERT: A 1214 ASP cc_start: 0.8133 (m-30) cc_final: 0.7849 (m-30) outliers start: 20 outliers final: 6 residues processed: 90 average time/residue: 0.6632 time to fit residues: 63.5454 Evaluate side-chains 82 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 364 THR 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 900 GLU 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: 0.4980 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.158902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118111 restraints weight = 12668.121| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.36 r_work: 0.3273 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2159 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= 0.133 Angle : 0.577 8.978 13592 Z= 0.299 Chirality : 0.039 0.221 1506 Planarity : 0.003 0.042 1548 Dihedral : 20.008 177.491 2003 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.41 % Allowed : 30.08 % 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: 1.56 (0.27), residues: 1007 helix: 2.60 (0.20), residues: 664 sheet: -1.24 (0.96), residues: 30 loop : -2.43 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 949 TYR 0.024 0.001 TYR A 843 PHE 0.011 0.001 PHE A 909 TRP 0.023 0.001 TRP A 887 HIS 0.005 0.001 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9910) covalent geometry : angle 0.57743 (13592) hydrogen bonds : bond 0.05457 ( 497) hydrogen bonds : angle 3.13087 ( 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 95 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5458 (OUTLIER) cc_final: 0.5098 (pmm150) REVERT: A 445 LYS cc_start: 0.8474 (tmtm) cc_final: 0.8250 (tmmm) REVERT: A 732 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7597 (ttpt) REVERT: A 830 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6305 (pm20) REVERT: A 900 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: A 977 CYS cc_start: 0.7311 (m) cc_final: 0.7064 (m) REVERT: A 1200 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6845 (mp) REVERT: A 1214 ASP cc_start: 0.8150 (m-30) cc_final: 0.7869 (m-30) outliers start: 22 outliers final: 7 residues processed: 91 average time/residue: 0.6588 time to fit residues: 63.8322 Evaluate side-chains 80 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 364 THR 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 900 GLU Chi-restraints excluded: chain A residue 998 CYS 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: 6.9990 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.158541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118141 restraints weight = 12650.160| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.35 r_work: 0.3269 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9910 Z= 0.140 Angle : 0.609 10.048 13592 Z= 0.313 Chirality : 0.040 0.282 1506 Planarity : 0.003 0.045 1548 Dihedral : 19.992 177.339 2003 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.98 % Allowed : 30.74 % 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: 2.59 (0.20), residues: 664 sheet: -1.26 (0.95), residues: 30 loop : -2.46 (0.31), residues: 313 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 0.012 0.001 PHE A 909 TRP 0.027 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9910) covalent geometry : angle 0.60943 (13592) hydrogen bonds : bond 0.05458 ( 497) hydrogen bonds : angle 3.18109 ( 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 90 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.5089 (pmm150) REVERT: A 445 LYS cc_start: 0.8477 (tmtm) cc_final: 0.8254 (tmmm) REVERT: A 732 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7624 (ttpt) REVERT: A 830 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: A 977 CYS cc_start: 0.7256 (m) cc_final: 0.6999 (m) REVERT: A 1200 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6871 (mp) REVERT: A 1214 ASP cc_start: 0.8148 (m-30) cc_final: 0.7937 (m-30) outliers start: 18 outliers final: 7 residues processed: 87 average time/residue: 0.6655 time to fit residues: 61.5412 Evaluate side-chains 79 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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 998 CYS 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: 7.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.158026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117118 restraints weight = 12757.378| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.38 r_work: 0.3256 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9910 Z= 0.149 Angle : 0.617 9.081 13592 Z= 0.318 Chirality : 0.040 0.251 1506 Planarity : 0.003 0.041 1548 Dihedral : 20.000 176.943 2003 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % 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 : 0.00 % 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: 1.47 (0.27), residues: 1007 helix: 2.53 (0.20), residues: 664 sheet: -1.33 (0.94), residues: 30 loop : -2.46 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 949 TYR 0.026 0.001 TYR A 843 PHE 0.013 0.001 PHE A 909 TRP 0.025 0.002 TRP A 887 HIS 0.004 0.001 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9910) covalent geometry : angle 0.61675 (13592) hydrogen bonds : bond 0.05548 ( 497) hydrogen bonds : angle 3.22638 ( 1433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2691.08 seconds wall clock time: 46 minutes 38.54 seconds (2798.54 seconds total)