Starting phenix.real_space_refine on Wed Mar 4 04:14:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qfq_13947/03_2026/7qfq_13947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qfq_13947/03_2026/7qfq_13947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qfq_13947/03_2026/7qfq_13947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qfq_13947/03_2026/7qfq_13947.map" model { file = "/net/cci-nas-00/data/ceres_data/7qfq_13947/03_2026/7qfq_13947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qfq_13947/03_2026/7qfq_13947.cif" } resolution = 3.6 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= 0.034 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 6878 2.51 5 N 1714 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s 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: 10659 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1291, 10659 Classifications: {'peptide': 1291} Link IDs: {'PTRANS': 40, 'TRANS': 1250} Time building chain proxies: 2.38, per 1000 atoms: 0.22 Number of scatterers: 10659 At special positions: 0 Unit cell: (79.57, 128.62, 164.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 2032 8.00 N 1714 7.00 C 6878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 446 " distance=2.04 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: 0.87 Conformation dependent library (CDL) restraints added in 424.4 milliseconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 18 sheets defined 32.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 81 through 102 removed outlier: 4.414A pdb=" N LYS A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.776A pdb=" N HIS A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.898A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.700A pdb=" N ILE A 280 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 306 Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 409 through 412 removed outlier: 3.619A pdb=" N GLN A 412 " --> pdb=" O TYR A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 412' Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.719A pdb=" N ASN A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 418' Processing helix chain 'A' and resid 459 through 463 removed outlier: 3.743A pdb=" N PHE A 463 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.875A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 589 through 606 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 638 through 647 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 677 through 741 removed outlier: 4.640A pdb=" N ASN A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR A 741 " --> pdb=" O ARG A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 removed outlier: 3.947A pdb=" N LYS A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 787 removed outlier: 4.363A pdb=" N ILE A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 813 removed outlier: 3.904A pdb=" N ALA A 791 " --> pdb=" O MET A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 821 through 831 Processing helix chain 'A' and resid 839 through 844 removed outlier: 4.236A pdb=" N TYR A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 859 removed outlier: 3.702A pdb=" N ILE A 850 " --> pdb=" O ASP A 846 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 947 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1263 through 1270 removed outlier: 4.455A pdb=" N VAL A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 22 removed outlier: 7.013A pdb=" N ILE A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP A 44 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 141 removed outlier: 3.631A pdb=" N THR A 508 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 221 removed outlier: 6.665A pdb=" N VAL A 200 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 202 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 331 through 332 removed outlier: 3.590A pdb=" N VAL A 331 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 446 through 450 removed outlier: 7.219A pdb=" N LYS A 433 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE A 530 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN A 435 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 472 removed outlier: 7.008A pdb=" N GLU A 471 " --> pdb=" O LEU A 667 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 556 removed outlier: 3.758A pdb=" N VAL A 569 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 868 through 870 removed outlier: 4.079A pdb=" N ARG A 869 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 876 " --> pdb=" O ARG A 869 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 884 through 886 Processing sheet with id=AB2, first strand: chain 'A' and resid 899 through 901 removed outlier: 3.735A pdb=" N ALA A1014 " --> pdb=" O THR A1026 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A1026 " --> pdb=" O ALA A1014 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A1016 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER A1024 " --> pdb=" O ILE A1016 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 899 through 901 Processing sheet with id=AB4, first strand: chain 'A' and resid 982 through 987 removed outlier: 3.617A pdb=" N LYS A 983 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 970 " --> pdb=" O ARG A 967 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 953 " --> pdb=" O ILE A 964 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 966 " --> pdb=" O THR A 951 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR A 951 " --> pdb=" O ILE A 966 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN A 954 " --> pdb=" O ILE A1041 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A1041 " --> pdb=" O ASN A 954 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 3.804A pdb=" N TYR A1109 " --> pdb=" O LEU A1122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1122 " --> pdb=" O TYR A1109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1172 through 1173 Processing sheet with id=AB7, first strand: chain 'A' and resid 1179 through 1181 Processing sheet with id=AB8, first strand: chain 'A' and resid 1208 through 1211 Processing sheet with id=AB9, first strand: chain 'A' and resid 1238 through 1245 removed outlier: 3.677A pdb=" N GLU A1252 " --> pdb=" O GLU A1245 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3395 1.35 - 1.47: 2693 1.47 - 1.60: 4745 1.60 - 1.72: 0 1.72 - 1.85: 60 Bond restraints: 10893 Sorted by residual: bond pdb=" N ASN A 873 " pdb=" CA ASN A 873 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.41e+00 bond pdb=" CB CYS A 446 " pdb=" SG CYS A 446 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" C ILE A 310 " pdb=" O ILE A 310 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.73e-01 bond pdb=" CG PRO A 313 " pdb=" CD PRO A 313 " ideal model delta sigma weight residual 1.503 1.534 -0.031 3.40e-02 8.65e+02 8.47e-01 bond pdb=" CG LEU A 232 " pdb=" CD1 LEU A 232 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.34e-01 ... (remaining 10888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 14451 1.68 - 3.36: 224 3.36 - 5.04: 33 5.04 - 6.72: 6 6.72 - 8.40: 2 Bond angle restraints: 14716 Sorted by residual: angle pdb=" N ILE A1018 " pdb=" CA ILE A1018 " pdb=" C ILE A1018 " ideal model delta sigma weight residual 113.53 108.95 4.58 9.80e-01 1.04e+00 2.19e+01 angle pdb=" N LYS A 418 " pdb=" CA LYS A 418 " pdb=" CB LYS A 418 " ideal model delta sigma weight residual 113.65 108.77 4.88 1.47e+00 4.63e-01 1.10e+01 angle pdb=" C LYS A 675 " pdb=" N ASN A 676 " pdb=" CA ASN A 676 " ideal model delta sigma weight residual 122.46 127.08 -4.62 1.41e+00 5.03e-01 1.07e+01 angle pdb=" CA MET A 956 " pdb=" CB MET A 956 " pdb=" CG MET A 956 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.43e+00 angle pdb=" C MET A1056 " pdb=" N LYS A1057 " pdb=" CA LYS A1057 " ideal model delta sigma weight residual 122.17 117.84 4.33 1.54e+00 4.22e-01 7.90e+00 ... (remaining 14711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5959 17.82 - 35.63: 521 35.63 - 53.45: 75 53.45 - 71.27: 7 71.27 - 89.09: 5 Dihedral angle restraints: 6567 sinusoidal: 2728 harmonic: 3839 Sorted by residual: dihedral pdb=" CA ASN A 417 " pdb=" C ASN A 417 " pdb=" N LYS A 418 " pdb=" CA LYS A 418 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ILE A 932 " pdb=" C ILE A 932 " pdb=" N ARG A 933 " pdb=" CA ARG A 933 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA THR A 707 " pdb=" C THR A 707 " pdb=" N VAL A 708 " pdb=" CA VAL A 708 " ideal model delta harmonic sigma weight residual 180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1214 0.047 - 0.095: 263 0.095 - 0.142: 104 0.142 - 0.189: 3 0.189 - 0.236: 1 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CB ILE A 46 " pdb=" CA ILE A 46 " pdb=" CG1 ILE A 46 " pdb=" CG2 ILE A 46 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CG LEU A1237 " pdb=" CB LEU A1237 " pdb=" CD1 LEU A1237 " pdb=" CD2 LEU A1237 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ASN A 873 " pdb=" N ASN A 873 " pdb=" C ASN A 873 " pdb=" CB ASN A 873 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1582 not shown) Planarity restraints: 1893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 312 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO A 313 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 934 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 935 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 935 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 935 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 223 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.50e+00 pdb=" N PRO A 224 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " -0.022 5.00e-02 4.00e+02 ... (remaining 1890 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 363 2.72 - 3.27: 10482 3.27 - 3.81: 15569 3.81 - 4.36: 18190 4.36 - 4.90: 31984 Nonbonded interactions: 76588 Sorted by model distance: nonbonded pdb=" OG1 THR A 951 " pdb=" O ILE A 964 " model vdw 2.177 3.040 nonbonded pdb=" OE2 GLU A 253 " pdb=" OG SER A 260 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR A1080 " pdb=" OE2 GLU A1082 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP A 346 " pdb=" NZ LYS A 350 " model vdw 2.262 3.120 nonbonded pdb=" NH2 ARG A 933 " pdb=" OD1 ASN A1000 " model vdw 2.269 3.120 ... (remaining 76583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 2.340 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.320 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: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 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 : 0.002 0.037 10894 Z= 0.120 Angle : 0.544 8.396 14718 Z= 0.303 Chirality : 0.044 0.236 1585 Planarity : 0.004 0.078 1893 Dihedral : 12.927 89.086 4098 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.70 (0.24), residues: 1289 helix: 2.15 (0.29), residues: 364 sheet: -0.93 (0.43), residues: 157 loop : -1.79 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 933 TYR 0.018 0.001 TYR A 540 PHE 0.018 0.001 PHE A 923 TRP 0.018 0.002 TRP A 693 HIS 0.001 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00240 (10893) covalent geometry : angle 0.54250 (14716) SS BOND : bond 0.00558 ( 1) SS BOND : angle 3.87442 ( 2) hydrogen bonds : bond 0.11396 ( 350) hydrogen bonds : angle 4.88619 ( 993) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.382 Fit side-chains REVERT: A 388 ASP cc_start: 0.7814 (t70) cc_final: 0.7437 (t0) REVERT: A 931 TRP cc_start: 0.8006 (m100) cc_final: 0.7480 (m-10) REVERT: A 1075 TYR cc_start: 0.8003 (t80) cc_final: 0.7544 (t80) REVERT: A 1100 MET cc_start: 0.5735 (tpt) cc_final: 0.5345 (tpt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0918 time to fit residues: 16.6805 Evaluate side-chains 103 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0010 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 709 ASN A 766 GLN A1052 GLN A1173 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.241345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.191143 restraints weight = 12214.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.182568 restraints weight = 15956.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.185985 restraints weight = 14325.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.186776 restraints weight = 9313.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.187131 restraints weight = 8391.173| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10894 Z= 0.158 Angle : 0.532 5.470 14718 Z= 0.289 Chirality : 0.045 0.220 1585 Planarity : 0.004 0.049 1893 Dihedral : 4.356 22.137 1411 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.01 % Allowed : 7.31 % Favored : 91.68 % 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: -0.86 (0.23), residues: 1289 helix: 2.01 (0.29), residues: 361 sheet: -1.15 (0.42), residues: 167 loop : -1.84 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 933 TYR 0.028 0.001 TYR A 741 PHE 0.017 0.002 PHE A 221 TRP 0.013 0.002 TRP A 693 HIS 0.007 0.002 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00378 (10893) covalent geometry : angle 0.53067 (14716) SS BOND : bond 0.00202 ( 1) SS BOND : angle 3.02162 ( 2) hydrogen bonds : bond 0.05944 ( 350) hydrogen bonds : angle 4.54089 ( 993) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.339 Fit side-chains REVERT: A 122 ARG cc_start: 0.6429 (ptt-90) cc_final: 0.5793 (ptt180) REVERT: A 174 ASP cc_start: 0.6845 (p0) cc_final: 0.6554 (p0) REVERT: A 388 ASP cc_start: 0.7447 (t70) cc_final: 0.7131 (t0) REVERT: A 873 ASN cc_start: 0.7115 (m-40) cc_final: 0.6588 (p0) REVERT: A 1075 TYR cc_start: 0.8211 (t80) cc_final: 0.7600 (t80) REVERT: A 1100 MET cc_start: 0.6170 (tpt) cc_final: 0.5497 (tpt) outliers start: 12 outliers final: 8 residues processed: 114 average time/residue: 0.0873 time to fit residues: 14.9069 Evaluate side-chains 104 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN A 476 ASN A 507 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.241381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.192733 restraints weight = 12291.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.189514 restraints weight = 19591.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.191913 restraints weight = 16816.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.192529 restraints weight = 10049.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.193316 restraints weight = 8838.482| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10894 Z= 0.138 Angle : 0.496 5.025 14718 Z= 0.270 Chirality : 0.044 0.172 1585 Planarity : 0.004 0.042 1893 Dihedral : 4.297 23.962 1411 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.43 % Allowed : 10.67 % Favored : 87.90 % 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: -0.85 (0.24), residues: 1289 helix: 2.05 (0.29), residues: 362 sheet: -1.21 (0.42), residues: 168 loop : -1.84 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 933 TYR 0.017 0.001 TYR A 421 PHE 0.015 0.001 PHE A 221 TRP 0.013 0.001 TRP A 693 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00327 (10893) covalent geometry : angle 0.49531 (14716) SS BOND : bond 0.00217 ( 1) SS BOND : angle 2.31063 ( 2) hydrogen bonds : bond 0.05829 ( 350) hydrogen bonds : angle 4.40993 ( 993) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.263 Fit side-chains REVERT: A 172 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8141 (p) REVERT: A 388 ASP cc_start: 0.7314 (t70) cc_final: 0.7029 (t0) REVERT: A 852 MET cc_start: 0.2824 (tpt) cc_final: 0.1637 (ptt) REVERT: A 873 ASN cc_start: 0.6888 (m-40) cc_final: 0.6516 (p0) REVERT: A 1075 TYR cc_start: 0.8002 (t80) cc_final: 0.7532 (t80) REVERT: A 1100 MET cc_start: 0.6300 (tpt) cc_final: 0.5488 (tpt) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.0808 time to fit residues: 12.9382 Evaluate side-chains 109 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.241988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.194224 restraints weight = 12358.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.192466 restraints weight = 17613.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.193328 restraints weight = 17316.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.193812 restraints weight = 10026.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.194424 restraints weight = 8470.907| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10894 Z= 0.122 Angle : 0.475 5.511 14718 Z= 0.259 Chirality : 0.044 0.148 1585 Planarity : 0.003 0.040 1893 Dihedral : 4.179 22.392 1411 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.85 % Allowed : 12.61 % Favored : 85.55 % 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: -0.80 (0.24), residues: 1289 helix: 2.11 (0.29), residues: 362 sheet: -1.10 (0.42), residues: 163 loop : -1.84 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 933 TYR 0.019 0.001 TYR A 421 PHE 0.018 0.001 PHE A1004 TRP 0.013 0.001 TRP A 693 HIS 0.002 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00286 (10893) covalent geometry : angle 0.47388 (14716) SS BOND : bond 0.00282 ( 1) SS BOND : angle 2.30605 ( 2) hydrogen bonds : bond 0.05569 ( 350) hydrogen bonds : angle 4.29696 ( 993) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.357 Fit side-chains REVERT: A 172 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8079 (p) REVERT: A 218 ARG cc_start: 0.7721 (ptt180) cc_final: 0.7472 (ptt-90) REVERT: A 388 ASP cc_start: 0.7281 (t70) cc_final: 0.7003 (t0) REVERT: A 852 MET cc_start: 0.2663 (tpt) cc_final: 0.1562 (ptt) REVERT: A 873 ASN cc_start: 0.6733 (m-40) cc_final: 0.6366 (p0) REVERT: A 1075 TYR cc_start: 0.7990 (t80) cc_final: 0.7553 (t80) REVERT: A 1099 TYR cc_start: 0.7418 (m-80) cc_final: 0.7078 (m-10) outliers start: 22 outliers final: 16 residues processed: 117 average time/residue: 0.0955 time to fit residues: 16.2301 Evaluate side-chains 108 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 606 ASN A 766 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.239076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.195543 restraints weight = 12307.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191187 restraints weight = 22004.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.193319 restraints weight = 20766.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.193599 restraints weight = 12320.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.194420 restraints weight = 10548.015| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10894 Z= 0.165 Angle : 0.530 6.480 14718 Z= 0.286 Chirality : 0.045 0.151 1585 Planarity : 0.004 0.042 1893 Dihedral : 4.324 23.343 1411 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.18 % Allowed : 13.95 % Favored : 83.87 % 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: -0.94 (0.24), residues: 1289 helix: 1.95 (0.28), residues: 362 sheet: -1.20 (0.43), residues: 163 loop : -1.89 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1074 TYR 0.027 0.001 TYR A 421 PHE 0.018 0.002 PHE A 221 TRP 0.016 0.002 TRP A1002 HIS 0.012 0.002 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00404 (10893) covalent geometry : angle 0.52939 (14716) SS BOND : bond 0.00161 ( 1) SS BOND : angle 1.94373 ( 2) hydrogen bonds : bond 0.06264 ( 350) hydrogen bonds : angle 4.45195 ( 993) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.403 Fit side-chains REVERT: A 218 ARG cc_start: 0.7720 (ptt180) cc_final: 0.7441 (ptt-90) REVERT: A 388 ASP cc_start: 0.7425 (t70) cc_final: 0.7225 (t0) REVERT: A 852 MET cc_start: 0.2747 (tpt) cc_final: 0.1575 (ptt) REVERT: A 873 ASN cc_start: 0.6692 (m-40) cc_final: 0.6372 (p0) REVERT: A 1075 TYR cc_start: 0.7988 (t80) cc_final: 0.7610 (t80) REVERT: A 1099 TYR cc_start: 0.7454 (m-80) cc_final: 0.7229 (m-10) outliers start: 26 outliers final: 18 residues processed: 118 average time/residue: 0.0904 time to fit residues: 15.8675 Evaluate side-chains 109 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 123 optimal weight: 0.0570 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 115 optimal weight: 0.3980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.239347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.189106 restraints weight = 12162.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.183634 restraints weight = 17093.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.186671 restraints weight = 14820.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.187776 restraints weight = 8669.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.188705 restraints weight = 7692.811| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10894 Z= 0.102 Angle : 0.458 6.359 14718 Z= 0.250 Chirality : 0.043 0.140 1585 Planarity : 0.003 0.039 1893 Dihedral : 4.061 22.302 1411 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.60 % Allowed : 14.54 % Favored : 83.87 % 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: -0.72 (0.24), residues: 1289 helix: 2.24 (0.29), residues: 362 sheet: -1.20 (0.42), residues: 163 loop : -1.78 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 933 TYR 0.018 0.001 TYR A 421 PHE 0.015 0.001 PHE A1004 TRP 0.014 0.001 TRP A 693 HIS 0.002 0.000 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00220 (10893) covalent geometry : angle 0.45764 (14716) SS BOND : bond 0.00284 ( 1) SS BOND : angle 2.35941 ( 2) hydrogen bonds : bond 0.05187 ( 350) hydrogen bonds : angle 4.18563 ( 993) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.390 Fit side-chains REVERT: A 218 ARG cc_start: 0.7732 (ptt180) cc_final: 0.7525 (ptt-90) REVERT: A 852 MET cc_start: 0.2487 (tpt) cc_final: 0.1591 (ptt) REVERT: A 873 ASN cc_start: 0.6999 (m-40) cc_final: 0.6359 (p0) REVERT: A 1075 TYR cc_start: 0.8069 (t80) cc_final: 0.7669 (t80) REVERT: A 1099 TYR cc_start: 0.7389 (m-80) cc_final: 0.7179 (m-10) outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.0965 time to fit residues: 15.4269 Evaluate side-chains 106 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 119 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 62 optimal weight: 0.0170 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.242816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.192984 restraints weight = 12276.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.186861 restraints weight = 16432.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.190459 restraints weight = 15885.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.190740 restraints weight = 9426.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.191261 restraints weight = 8329.648| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10894 Z= 0.106 Angle : 0.459 6.726 14718 Z= 0.249 Chirality : 0.043 0.140 1585 Planarity : 0.003 0.041 1893 Dihedral : 4.001 21.913 1411 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.76 % Allowed : 14.62 % Favored : 83.61 % 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: -0.70 (0.24), residues: 1289 helix: 2.23 (0.29), residues: 362 sheet: -1.23 (0.41), residues: 163 loop : -1.74 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 933 TYR 0.018 0.001 TYR A 421 PHE 0.017 0.001 PHE A 930 TRP 0.013 0.001 TRP A 693 HIS 0.002 0.000 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00239 (10893) covalent geometry : angle 0.45814 (14716) SS BOND : bond 0.00223 ( 1) SS BOND : angle 2.39920 ( 2) hydrogen bonds : bond 0.05126 ( 350) hydrogen bonds : angle 4.12500 ( 993) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.418 Fit side-chains REVERT: A 218 ARG cc_start: 0.7740 (ptt180) cc_final: 0.7498 (ptt-90) REVERT: A 741 TYR cc_start: 0.6836 (t80) cc_final: 0.6602 (t80) REVERT: A 852 MET cc_start: 0.2424 (tpt) cc_final: 0.1608 (ptt) REVERT: A 873 ASN cc_start: 0.7013 (m-40) cc_final: 0.6354 (p0) REVERT: A 1075 TYR cc_start: 0.8059 (t80) cc_final: 0.7694 (t80) REVERT: A 1099 TYR cc_start: 0.7366 (m-80) cc_final: 0.7128 (m-10) REVERT: A 1137 ARG cc_start: 0.4307 (OUTLIER) cc_final: 0.4082 (ptt90) outliers start: 21 outliers final: 16 residues processed: 108 average time/residue: 0.1025 time to fit residues: 16.3057 Evaluate side-chains 108 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1137 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1019 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 = 0.4760 r_free = 0.4760 target = 0.241959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.193021 restraints weight = 12262.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.187251 restraints weight = 18478.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.190537 restraints weight = 16959.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.191000 restraints weight = 9661.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.191706 restraints weight = 9129.534| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10894 Z= 0.118 Angle : 0.478 7.221 14718 Z= 0.258 Chirality : 0.043 0.138 1585 Planarity : 0.003 0.046 1893 Dihedral : 4.010 22.834 1411 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.93 % Allowed : 14.71 % Favored : 83.36 % 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: -0.71 (0.24), residues: 1289 helix: 2.20 (0.29), residues: 362 sheet: -1.23 (0.42), residues: 163 loop : -1.73 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 967 TYR 0.014 0.001 TYR A 421 PHE 0.014 0.001 PHE A 930 TRP 0.014 0.001 TRP A1002 HIS 0.002 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00276 (10893) covalent geometry : angle 0.47757 (14716) SS BOND : bond 0.00243 ( 1) SS BOND : angle 2.50491 ( 2) hydrogen bonds : bond 0.05297 ( 350) hydrogen bonds : angle 4.12702 ( 993) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.360 Fit side-chains REVERT: A 172 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8038 (p) REVERT: A 218 ARG cc_start: 0.7729 (ptt180) cc_final: 0.7464 (ptt-90) REVERT: A 852 MET cc_start: 0.2471 (tpt) cc_final: 0.1620 (ptt) REVERT: A 873 ASN cc_start: 0.6905 (m-40) cc_final: 0.6334 (p0) REVERT: A 1058 TYR cc_start: 0.6670 (m-10) cc_final: 0.6433 (m-10) REVERT: A 1075 TYR cc_start: 0.8003 (t80) cc_final: 0.7644 (t80) REVERT: A 1100 MET cc_start: 0.6570 (tpt) cc_final: 0.5939 (tpp) outliers start: 23 outliers final: 17 residues processed: 112 average time/residue: 0.1024 time to fit residues: 16.7710 Evaluate side-chains 111 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 0.0020 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 51 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 overall best weight: 0.3624 ------------------------------------------------------------------------------- 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 = 0.4782 r_free = 0.4782 target = 0.244854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.198343 restraints weight = 12177.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.194713 restraints weight = 19756.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.197357 restraints weight = 17003.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.197566 restraints weight = 10191.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.198089 restraints weight = 8752.223| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10894 Z= 0.096 Angle : 0.453 7.379 14718 Z= 0.246 Chirality : 0.042 0.140 1585 Planarity : 0.003 0.045 1893 Dihedral : 3.847 21.794 1411 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.60 % Allowed : 15.38 % Favored : 83.03 % 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: -0.59 (0.24), residues: 1289 helix: 2.32 (0.29), residues: 362 sheet: -1.23 (0.40), residues: 173 loop : -1.65 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 970 TYR 0.031 0.001 TYR A1099 PHE 0.013 0.001 PHE A 930 TRP 0.016 0.001 TRP A 693 HIS 0.001 0.000 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00210 (10893) covalent geometry : angle 0.45150 (14716) SS BOND : bond 0.00270 ( 1) SS BOND : angle 2.71481 ( 2) hydrogen bonds : bond 0.04664 ( 350) hydrogen bonds : angle 3.98585 ( 993) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.414 Fit side-chains REVERT: A 172 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.7962 (p) REVERT: A 218 ARG cc_start: 0.7763 (ptt180) cc_final: 0.7554 (ptt-90) REVERT: A 478 GLN cc_start: 0.7356 (tp-100) cc_final: 0.6440 (pm20) REVERT: A 680 LYS cc_start: 0.7436 (mmtp) cc_final: 0.7190 (mmmm) REVERT: A 852 MET cc_start: 0.2330 (tpt) cc_final: 0.1514 (ptt) REVERT: A 873 ASN cc_start: 0.6789 (m-40) cc_final: 0.6296 (p0) REVERT: A 1058 TYR cc_start: 0.6648 (m-10) cc_final: 0.6415 (m-10) REVERT: A 1075 TYR cc_start: 0.7904 (t80) cc_final: 0.7597 (t80) outliers start: 19 outliers final: 17 residues processed: 108 average time/residue: 0.0952 time to fit residues: 15.4163 Evaluate side-chains 110 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 122 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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 = 0.4754 r_free = 0.4754 target = 0.240918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.193532 restraints weight = 12261.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.187868 restraints weight = 20530.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.191173 restraints weight = 18613.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.191454 restraints weight = 10593.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.192167 restraints weight = 9966.145| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10894 Z= 0.139 Angle : 0.506 10.473 14718 Z= 0.270 Chirality : 0.044 0.145 1585 Planarity : 0.003 0.049 1893 Dihedral : 4.008 22.139 1411 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.76 % Allowed : 15.13 % Favored : 83.11 % 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: -0.71 (0.24), residues: 1289 helix: 2.12 (0.29), residues: 368 sheet: -1.27 (0.40), residues: 173 loop : -1.71 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1137 TYR 0.021 0.001 TYR A1099 PHE 0.015 0.001 PHE A 221 TRP 0.017 0.001 TRP A1002 HIS 0.002 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00332 (10893) covalent geometry : angle 0.50506 (14716) SS BOND : bond 0.00301 ( 1) SS BOND : angle 3.02798 ( 2) hydrogen bonds : bond 0.05486 ( 350) hydrogen bonds : angle 4.11907 ( 993) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.350 Fit side-chains REVERT: A 172 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 218 ARG cc_start: 0.7824 (ptt180) cc_final: 0.7562 (ptt-90) REVERT: A 478 GLN cc_start: 0.7345 (tp-100) cc_final: 0.6392 (pm20) REVERT: A 852 MET cc_start: 0.2502 (tpt) cc_final: 0.1605 (ptt) REVERT: A 873 ASN cc_start: 0.6898 (m-40) cc_final: 0.6329 (p0) REVERT: A 1058 TYR cc_start: 0.6692 (m-10) cc_final: 0.6471 (m-10) REVERT: A 1075 TYR cc_start: 0.7987 (t80) cc_final: 0.7612 (t80) REVERT: A 1100 MET cc_start: 0.6625 (tpt) cc_final: 0.5952 (tpp) outliers start: 21 outliers final: 18 residues processed: 108 average time/residue: 0.0930 time to fit residues: 14.9895 Evaluate side-chains 109 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1071 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4733 r_free = 0.4733 target = 0.238415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.192350 restraints weight = 12354.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.188414 restraints weight = 20470.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.190900 restraints weight = 17439.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.191141 restraints weight = 10496.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.192009 restraints weight = 9074.928| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10894 Z= 0.167 Angle : 0.532 7.218 14718 Z= 0.287 Chirality : 0.045 0.148 1585 Planarity : 0.004 0.050 1893 Dihedral : 4.220 23.402 1411 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.76 % Allowed : 15.38 % Favored : 82.86 % 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 (0.24), residues: 1289 helix: 1.89 (0.28), residues: 368 sheet: -1.35 (0.40), residues: 173 loop : -1.79 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1137 TYR 0.027 0.001 TYR A 421 PHE 0.023 0.002 PHE A1004 TRP 0.020 0.002 TRP A1002 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00405 (10893) covalent geometry : angle 0.53021 (14716) SS BOND : bond 0.00313 ( 1) SS BOND : angle 3.33280 ( 2) hydrogen bonds : bond 0.06175 ( 350) hydrogen bonds : angle 4.32064 ( 993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1603.29 seconds wall clock time: 28 minutes 30.49 seconds (1710.49 seconds total)