Starting phenix.real_space_refine on Sat Oct 11 10:57:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qmp_18506/10_2025/8qmp_18506.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qmp_18506/10_2025/8qmp_18506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qmp_18506/10_2025/8qmp_18506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qmp_18506/10_2025/8qmp_18506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qmp_18506/10_2025/8qmp_18506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qmp_18506/10_2025/8qmp_18506.map" } resolution = 3.3 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= -0.001 sd= 0.026 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: 8 Type Number sf(0) Gaussians Mg 1 5.21 5 S 33 5.16 5 Be 1 3.05 5 C 4392 2.51 5 N 1174 2.21 5 O 1307 1.98 5 F 3 1.80 5 H 7087 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13998 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 13993 Classifications: {'peptide': 913} Link IDs: {'PTRANS': 30, 'TRANS': 882} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.67, per 1000 atoms: 0.19 Number of scatterers: 13998 At special positions: 0 Unit cell: (74.6476, 89.3669, 142.987, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 33 16.00 Mg 1 11.99 F 3 9.00 O 1307 8.00 N 1174 7.00 C 4392 6.00 Be 1 4.00 H 7087 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 684 " - pdb=" SG CYS A 720 " distance=2.03 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: 1.43 Conformation dependent library (CDL) restraints added in 348.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 54.5% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.662A pdb=" N ILE A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.924A pdb=" N ARG A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 191 through 213 Processing helix chain 'A' and resid 218 through 251 removed outlier: 4.406A pdb=" N SER A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 342 through 345 removed outlier: 3.627A pdb=" N ASN A 345 " --> pdb=" O VAL A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 363 through 398 Processing helix chain 'A' and resid 422 through 438 removed outlier: 3.755A pdb=" N VAL A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 460 Processing helix chain 'A' and resid 468 through 473 removed outlier: 3.555A pdb=" N MET A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 524 removed outlier: 4.002A pdb=" N LEU A 516 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 556 Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 601 through 607 Processing helix chain 'A' and resid 622 through 639 Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 709 through 721 Processing helix chain 'A' and resid 736 through 743 removed outlier: 3.838A pdb=" N MET A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 776 Processing helix chain 'A' and resid 786 through 788 No H-bonds generated for 'chain 'A' and resid 786 through 788' Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 823 through 866 Processing helix chain 'A' and resid 871 through 892 removed outlier: 4.428A pdb=" N LEU A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.663A pdb=" N GLY A 901 " --> pdb=" O ASP A 897 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 902 " --> pdb=" O HIS A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 902' Processing helix chain 'A' and resid 913 through 942 removed outlier: 6.586A pdb=" N ILE A 939 " --> pdb=" O ASN A 935 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 977 removed outlier: 3.960A pdb=" N LYS A 977 " --> pdb=" O PHE A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1007 Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1034 through 1045 removed outlier: 3.867A pdb=" N LEU A1038 " --> pdb=" O ILE A1034 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 279 through 282 removed outlier: 3.662A pdb=" N CYS A 328 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 282 removed outlier: 3.538A pdb=" N LYS A 329 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA A 301 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY A 333 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N SER A 299 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 335 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 297 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET A 337 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE A 295 " --> pdb=" O MET A 337 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL A 339 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A 293 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 464 removed outlier: 6.002A pdb=" N GLY A 799 " --> pdb=" O ILE A 816 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE A 818 " --> pdb=" O GLY A 799 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA A 801 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 780 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU A 800 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 782 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N MET A 802 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLY A 784 " --> pdb=" O MET A 802 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 478 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N THR A 783 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS A 480 " --> pdb=" O THR A 783 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N MET A 758 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET A 704 " --> pdb=" O MET A 758 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 497 removed outlier: 7.183A pdb=" N GLY A 679 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER A 497 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 677 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU A 674 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 648 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 676 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS A 571 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS A 587 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 569 " --> pdb=" O LYS A 587 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 497 removed outlier: 7.183A pdb=" N GLY A 679 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER A 497 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 677 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 672 " --> pdb=" O CYS A 608 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 676 " --> pdb=" O ILE A 612 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1170 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: 3.55 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7078 1.03 - 1.23: 12 1.23 - 1.42: 2753 1.42 - 1.62: 4205 1.62 - 1.81: 55 Bond restraints: 14103 Sorted by residual: bond pdb=" CG LEU A 875 " pdb=" CD1 LEU A 875 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.13e-01 bond pdb=" CG LEU A 207 " pdb=" CD1 LEU A 207 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.03e-01 bond pdb=" CB THR A 958 " pdb=" CG2 THR A 958 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.13e-01 bond pdb=" CB PHE A 184 " pdb=" CG PHE A 184 " ideal model delta sigma weight residual 1.502 1.518 -0.016 2.30e-02 1.89e+03 4.67e-01 bond pdb=" CB THR A 428 " pdb=" CG2 THR A 428 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.58e-01 ... (remaining 14098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.12: 25632 6.12 - 12.24: 2 12.24 - 18.36: 0 18.36 - 24.48: 0 24.48 - 30.60: 5 Bond angle restraints: 25639 Sorted by residual: angle pdb=" CG LYS A 681 " pdb=" CB LYS A 681 " pdb=" HB2 LYS A 681 " ideal model delta sigma weight residual 108.00 77.40 30.60 3.00e+00 1.11e-01 1.04e+02 angle pdb=" CA LYS A 681 " pdb=" CB LYS A 681 " pdb=" HB2 LYS A 681 " ideal model delta sigma weight residual 109.00 79.74 29.26 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CA LYS A 681 " pdb=" CB LYS A 681 " pdb=" HB3 LYS A 681 " ideal model delta sigma weight residual 109.00 81.22 27.78 3.00e+00 1.11e-01 8.57e+01 angle pdb=" CG LYS A 681 " pdb=" CB LYS A 681 " pdb=" HB3 LYS A 681 " ideal model delta sigma weight residual 108.00 80.89 27.11 3.00e+00 1.11e-01 8.17e+01 angle pdb=" HB2 LYS A 681 " pdb=" CB LYS A 681 " pdb=" HB3 LYS A 681 " ideal model delta sigma weight residual 110.00 136.25 -26.25 3.00e+00 1.11e-01 7.65e+01 ... (remaining 25634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5656 17.65 - 35.30: 611 35.30 - 52.95: 199 52.95 - 70.60: 63 70.60 - 88.25: 8 Dihedral angle restraints: 6537 sinusoidal: 3641 harmonic: 2896 Sorted by residual: dihedral pdb=" CB CYS A 684 " pdb=" SG CYS A 684 " pdb=" SG CYS A 720 " pdb=" CB CYS A 720 " ideal model delta sinusoidal sigma weight residual -86.00 -144.00 58.00 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CA ALA A 459 " pdb=" C ALA A 459 " pdb=" N ASP A 460 " pdb=" CA ASP A 460 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP A 158 " pdb=" CB ASP A 158 " pdb=" CG ASP A 158 " pdb=" OD1 ASP A 158 " ideal model delta sinusoidal sigma weight residual -30.00 -89.35 59.35 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 6534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 702 0.028 - 0.056: 279 0.056 - 0.084: 103 0.084 - 0.112: 51 0.112 - 0.140: 15 Chirality restraints: 1150 Sorted by residual: chirality pdb=" CA ILE A 735 " pdb=" N ILE A 735 " pdb=" C ILE A 735 " pdb=" CB ILE A 735 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE A 816 " pdb=" N ILE A 816 " pdb=" C ILE A 816 " pdb=" CB ILE A 816 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE A 673 " pdb=" N ILE A 673 " pdb=" C ILE A 673 " pdb=" CB ILE A 673 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1147 not shown) Planarity restraints: 2085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 879 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C ASN A 879 " 0.021 2.00e-02 2.50e+03 pdb=" O ASN A 879 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 880 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 843 " -0.014 2.00e-02 2.50e+03 6.65e-03 1.33e+00 pdb=" CG PHE A 843 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 843 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 843 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 843 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 843 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 843 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 843 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 843 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 843 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 843 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 843 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 118 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C PRO A 118 " -0.017 2.00e-02 2.50e+03 pdb=" O PRO A 118 " 0.007 2.00e-02 2.50e+03 pdb=" N GLU A 119 " 0.006 2.00e-02 2.50e+03 ... (remaining 2082 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 172 2.03 - 2.67: 21819 2.67 - 3.32: 42460 3.32 - 3.96: 53405 3.96 - 4.60: 83562 Nonbonded interactions: 201418 Sorted by model distance: nonbonded pdb=" OD1 ASP A 482 " pdb=" F3 BEF A1102 " model vdw 1.392 2.870 nonbonded pdb=" OD1 ASP A 482 " pdb="BE BEF A1102 " model vdw 1.400 2.300 nonbonded pdb=" OD1 ASP A 749 " pdb=" HG SER A 772 " model vdw 1.599 2.450 nonbonded pdb=" O LEU A 207 " pdb=" HG1 THR A 211 " model vdw 1.616 2.450 nonbonded pdb=" O GLY A 986 " pdb="HH22 ARG A 991 " model vdw 1.650 2.450 ... (remaining 201413 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 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: 1.100 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: 0.100 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.430 Find NCS groups from input model: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 : 0.003 0.030 7017 Z= 0.120 Angle : 0.504 9.130 9521 Z= 0.273 Chirality : 0.039 0.140 1150 Planarity : 0.003 0.022 1208 Dihedral : 16.723 88.254 2554 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 23.88 % Favored : 76.12 % 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 aren not related in a simple way. whole: 0.47 (0.28), residues: 909 helix: 1.84 (0.25), residues: 466 sheet: -1.36 (0.56), residues: 73 loop : -1.36 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 976 TYR 0.007 0.001 TYR A 926 PHE 0.018 0.001 PHE A 843 TRP 0.010 0.001 TRP A 348 HIS 0.002 0.000 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7016) covalent geometry : angle 0.50425 ( 9519) SS BOND : bond 0.00097 ( 1) SS BOND : angle 0.98498 ( 2) hydrogen bonds : bond 0.11308 ( 392) hydrogen bonds : angle 6.14610 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1477 time to fit residues: 21.7154 Evaluate side-chains 100 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 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 245 GLN ** 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 = 0.4362 r_free = 0.4362 target = 0.207139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.177185 restraints weight = 25230.377| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.38 r_work: 0.3913 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.0449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7017 Z= 0.150 Angle : 0.522 8.852 9521 Z= 0.285 Chirality : 0.040 0.147 1150 Planarity : 0.004 0.040 1208 Dihedral : 4.136 19.895 960 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.32 % Allowed : 22.43 % Favored : 76.25 % 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 aren not related in a simple way. whole: 0.34 (0.28), residues: 909 helix: 1.71 (0.24), residues: 476 sheet: -1.65 (0.57), residues: 67 loop : -1.45 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 685 TYR 0.009 0.001 TYR A 926 PHE 0.018 0.001 PHE A 843 TRP 0.012 0.001 TRP A 348 HIS 0.001 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7016) covalent geometry : angle 0.52211 ( 9519) SS BOND : bond 0.00177 ( 1) SS BOND : angle 1.08600 ( 2) hydrogen bonds : bond 0.04631 ( 392) hydrogen bonds : angle 5.44169 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 PHE cc_start: 0.7849 (t80) cc_final: 0.7588 (t80) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.1536 time to fit residues: 23.1489 Evaluate side-chains 102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 85 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 GLN ** 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 = 0.4365 r_free = 0.4365 target = 0.207569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177443 restraints weight = 25428.627| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.41 r_work: 0.3913 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7017 Z= 0.132 Angle : 0.506 8.912 9521 Z= 0.274 Chirality : 0.040 0.144 1150 Planarity : 0.003 0.034 1208 Dihedral : 4.141 19.849 960 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.19 % Allowed : 23.09 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.28), residues: 909 helix: 1.69 (0.24), residues: 477 sheet: -1.53 (0.55), residues: 73 loop : -1.50 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 703 TYR 0.009 0.001 TYR A 926 PHE 0.018 0.001 PHE A 843 TRP 0.011 0.001 TRP A 348 HIS 0.001 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7016) covalent geometry : angle 0.50577 ( 9519) SS BOND : bond 0.00154 ( 1) SS BOND : angle 1.03141 ( 2) hydrogen bonds : bond 0.04208 ( 392) hydrogen bonds : angle 5.22518 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 883 ASP cc_start: 0.4857 (m-30) cc_final: 0.4642 (m-30) outliers start: 9 outliers final: 7 residues processed: 103 average time/residue: 0.1325 time to fit residues: 20.9255 Evaluate side-chains 104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 chunk 10 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 GLN ** 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 = 0.4370 r_free = 0.4370 target = 0.208121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.178207 restraints weight = 25216.141| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.39 r_work: 0.3926 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7017 Z= 0.121 Angle : 0.495 9.120 9521 Z= 0.267 Chirality : 0.040 0.142 1150 Planarity : 0.003 0.028 1208 Dihedral : 4.106 19.640 960 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.58 % Allowed : 23.61 % Favored : 74.80 % 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 aren not related in a simple way. whole: 0.33 (0.28), residues: 909 helix: 1.73 (0.24), residues: 476 sheet: -1.52 (0.55), residues: 73 loop : -1.51 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 703 TYR 0.009 0.001 TYR A 926 PHE 0.018 0.001 PHE A 843 TRP 0.011 0.001 TRP A 348 HIS 0.001 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7016) covalent geometry : angle 0.49499 ( 9519) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.98281 ( 2) hydrogen bonds : bond 0.04005 ( 392) hydrogen bonds : angle 5.08052 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 ASP cc_start: 0.4847 (m-30) cc_final: 0.4643 (m-30) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.1467 time to fit residues: 23.2872 Evaluate side-chains 105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** 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 = 0.4354 r_free = 0.4354 target = 0.206426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176451 restraints weight = 25389.738| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.39 r_work: 0.3907 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7017 Z= 0.146 Angle : 0.513 8.692 9521 Z= 0.278 Chirality : 0.040 0.143 1150 Planarity : 0.003 0.030 1208 Dihedral : 4.166 20.178 960 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.72 % Allowed : 23.35 % Favored : 74.93 % 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 aren not related in a simple way. whole: 0.28 (0.27), residues: 909 helix: 1.68 (0.24), residues: 477 sheet: -1.59 (0.54), residues: 73 loop : -1.52 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 703 TYR 0.009 0.001 TYR A 926 PHE 0.018 0.001 PHE A 843 TRP 0.010 0.001 TRP A 348 HIS 0.002 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7016) covalent geometry : angle 0.51259 ( 9519) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.97016 ( 2) hydrogen bonds : bond 0.04070 ( 392) hydrogen bonds : angle 5.08334 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8336 (pp30) REVERT: A 868 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8451 (m) REVERT: A 883 ASP cc_start: 0.5027 (m-30) cc_final: 0.4802 (m-30) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.1528 time to fit residues: 25.4548 Evaluate side-chains 114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 997 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** 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 = 0.4347 r_free = 0.4347 target = 0.205489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.175429 restraints weight = 25349.130| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.39 r_work: 0.3897 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7017 Z= 0.155 Angle : 0.519 8.567 9521 Z= 0.282 Chirality : 0.040 0.145 1150 Planarity : 0.003 0.031 1208 Dihedral : 4.219 20.498 960 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.11 % Allowed : 23.22 % Favored : 74.67 % 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 aren not related in a simple way. whole: 0.26 (0.27), residues: 909 helix: 1.64 (0.24), residues: 477 sheet: -1.61 (0.56), residues: 67 loop : -1.51 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.009 0.001 TYR A 926 PHE 0.018 0.001 PHE A 843 TRP 0.010 0.001 TRP A 348 HIS 0.002 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7016) covalent geometry : angle 0.51902 ( 9519) SS BOND : bond 0.00137 ( 1) SS BOND : angle 1.01455 ( 2) hydrogen bonds : bond 0.04119 ( 392) hydrogen bonds : angle 5.07328 ( 1170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 868 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8469 (m) REVERT: A 883 ASP cc_start: 0.5039 (m-30) cc_final: 0.4801 (m-30) outliers start: 16 outliers final: 14 residues processed: 114 average time/residue: 0.1556 time to fit residues: 26.0489 Evaluate side-chains 117 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1038 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 29 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.206847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.176977 restraints weight = 25293.627| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.39 r_work: 0.3915 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7017 Z= 0.120 Angle : 0.496 8.867 9521 Z= 0.268 Chirality : 0.040 0.141 1150 Planarity : 0.003 0.030 1208 Dihedral : 4.137 19.867 960 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.98 % Allowed : 23.48 % Favored : 74.54 % 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 aren not related in a simple way. whole: 0.37 (0.28), residues: 909 helix: 1.73 (0.24), residues: 477 sheet: -1.58 (0.56), residues: 67 loop : -1.44 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.009 0.001 TYR A 926 PHE 0.018 0.001 PHE A 843 TRP 0.010 0.001 TRP A 348 HIS 0.001 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7016) covalent geometry : angle 0.49604 ( 9519) SS BOND : bond 0.00147 ( 1) SS BOND : angle 1.01271 ( 2) hydrogen bonds : bond 0.03950 ( 392) hydrogen bonds : angle 4.97876 ( 1170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 868 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8441 (m) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.1436 time to fit residues: 23.7053 Evaluate side-chains 114 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 962 ASN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1038 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** 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 = 0.4351 r_free = 0.4351 target = 0.206032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.176159 restraints weight = 25498.668| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.37 r_work: 0.3909 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7017 Z= 0.141 Angle : 0.509 8.577 9521 Z= 0.275 Chirality : 0.040 0.142 1150 Planarity : 0.003 0.031 1208 Dihedral : 4.162 20.320 960 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.37 % Allowed : 22.69 % Favored : 74.93 % 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 aren not related in a simple way. whole: 0.32 (0.28), residues: 909 helix: 1.69 (0.24), residues: 477 sheet: -1.62 (0.56), residues: 67 loop : -1.46 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.009 0.001 TYR A 926 PHE 0.018 0.001 PHE A 843 TRP 0.012 0.001 TRP A 348 HIS 0.002 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7016) covalent geometry : angle 0.50881 ( 9519) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.95901 ( 2) hydrogen bonds : bond 0.04003 ( 392) hydrogen bonds : angle 4.97787 ( 1170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 868 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8501 (m) REVERT: A 972 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7472 (tt0) outliers start: 18 outliers final: 16 residues processed: 114 average time/residue: 0.1519 time to fit residues: 25.5688 Evaluate side-chains 116 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 962 ASN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1038 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** 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 = 0.4345 r_free = 0.4345 target = 0.205490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.175570 restraints weight = 25414.338| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.38 r_work: 0.3905 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7017 Z= 0.140 Angle : 0.515 8.769 9521 Z= 0.277 Chirality : 0.040 0.141 1150 Planarity : 0.003 0.031 1208 Dihedral : 4.182 20.187 960 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.77 % Allowed : 22.43 % Favored : 74.80 % 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 aren not related in a simple way. whole: 0.28 (0.28), residues: 909 helix: 1.67 (0.24), residues: 477 sheet: -1.65 (0.56), residues: 67 loop : -1.49 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.009 0.001 TYR A 926 PHE 0.019 0.001 PHE A 843 TRP 0.012 0.001 TRP A 348 HIS 0.001 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7016) covalent geometry : angle 0.51439 ( 9519) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.94800 ( 2) hydrogen bonds : bond 0.03987 ( 392) hydrogen bonds : angle 4.96816 ( 1170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 LYS cc_start: 0.7838 (ttpp) cc_final: 0.7580 (ttpp) REVERT: A 868 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8509 (m) REVERT: A 972 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7522 (tt0) outliers start: 21 outliers final: 18 residues processed: 117 average time/residue: 0.1600 time to fit residues: 27.1800 Evaluate side-chains 121 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 962 ASN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1038 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** 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 = 0.4345 r_free = 0.4345 target = 0.205299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.175397 restraints weight = 25498.875| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.37 r_work: 0.3901 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7017 Z= 0.146 Angle : 0.520 8.605 9521 Z= 0.280 Chirality : 0.040 0.142 1150 Planarity : 0.003 0.031 1208 Dihedral : 4.208 20.466 960 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.90 % Allowed : 22.30 % Favored : 74.80 % 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 aren not related in a simple way. whole: 0.25 (0.28), residues: 909 helix: 1.66 (0.24), residues: 477 sheet: -1.72 (0.55), residues: 67 loop : -1.52 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.009 0.001 TYR A 926 PHE 0.018 0.001 PHE A 843 TRP 0.011 0.001 TRP A 348 HIS 0.002 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7016) covalent geometry : angle 0.51971 ( 9519) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.96658 ( 2) hydrogen bonds : bond 0.04014 ( 392) hydrogen bonds : angle 4.96739 ( 1170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 498 is missing expected H atoms. Skipping. Residue LYS 503 is missing expected H atoms. Skipping. Residue SER 691 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 LYS cc_start: 0.7824 (ttpp) cc_final: 0.7563 (ttpp) REVERT: A 868 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8501 (m) REVERT: A 972 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7464 (tt0) outliers start: 22 outliers final: 19 residues processed: 115 average time/residue: 0.1594 time to fit residues: 26.6184 Evaluate side-chains 121 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 962 ASN Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1038 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** 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 = 0.4346 r_free = 0.4346 target = 0.205541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175636 restraints weight = 25353.522| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.37 r_work: 0.3902 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7017 Z= 0.138 Angle : 0.515 8.683 9521 Z= 0.276 Chirality : 0.040 0.141 1150 Planarity : 0.003 0.031 1208 Dihedral : 4.219 20.248 960 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.64 % Allowed : 22.43 % Favored : 74.93 % 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 aren not related in a simple way. whole: 0.26 (0.28), residues: 909 helix: 1.67 (0.24), residues: 477 sheet: -1.71 (0.55), residues: 67 loop : -1.53 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.009 0.001 TYR A 926 PHE 0.019 0.001 PHE A 843 TRP 0.011 0.001 TRP A 348 HIS 0.002 0.000 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7016) covalent geometry : angle 0.51438 ( 9519) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.96493 ( 2) hydrogen bonds : bond 0.03973 ( 392) hydrogen bonds : angle 4.94677 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.29 seconds wall clock time: 61 minutes 56.70 seconds (3716.70 seconds total)