Starting phenix.real_space_refine on Sun Nov 17 15:47:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmp_18506/11_2024/8qmp_18506.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmp_18506/11_2024/8qmp_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmp_18506/11_2024/8qmp_18506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmp_18506/11_2024/8qmp_18506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmp_18506/11_2024/8qmp_18506.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qmp_18506/11_2024/8qmp_18506.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 6.81, per 1000 atoms: 0.49 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: 4.00 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.22 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: 5.84 Time building geometry restraints manager: 4.71 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: 1.200 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: 0.260 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- 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 7016 Z= 0.170 Angle : 0.504 9.130 9519 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 348 HIS 0.002 0.000 HIS A 946 PHE 0.018 0.001 PHE A 843 TYR 0.007 0.001 TYR A 926 ARG 0.001 0.000 ARG A 976 *********************** 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 : 1.089 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: 0.3528 time to fit residues: 51.6694 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 : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.0030 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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** A1004 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.0417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7016 Z= 0.166 Angle : 0.502 9.091 9519 Z= 0.273 Chirality : 0.040 0.145 1150 Planarity : 0.003 0.037 1208 Dihedral : 4.030 19.155 960 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.06 % Allowed : 22.96 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 909 helix: 1.81 (0.24), residues: 476 sheet: -1.58 (0.56), residues: 67 loop : -1.40 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 348 HIS 0.001 0.000 HIS A 778 PHE 0.018 0.001 PHE A 843 TYR 0.008 0.001 TYR A 926 ARG 0.003 0.000 ARG A 685 *********************** 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 110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 105 average time/residue: 0.3341 time to fit residues: 50.9329 Evaluate side-chains 104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 372 VAL Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 875 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** A1004 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7016 Z= 0.264 Angle : 0.540 8.690 9519 Z= 0.295 Chirality : 0.041 0.147 1150 Planarity : 0.003 0.033 1208 Dihedral : 4.250 20.886 960 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.58 % Allowed : 23.09 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 909 helix: 1.59 (0.24), residues: 477 sheet: -1.63 (0.55), residues: 73 loop : -1.57 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 348 HIS 0.003 0.001 HIS A 596 PHE 0.019 0.002 PHE A 843 TYR 0.009 0.001 TYR A 926 ARG 0.002 0.000 ARG A 262 *********************** 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 113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.3466 time to fit residues: 53.5577 Evaluate side-chains 110 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 519 GLU Chi-restraints excluded: chain A residue 593 VAL 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 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: