Starting phenix.real_space_refine on Mon Aug 25 05:49:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yrr_34065/08_2025/7yrr_34065.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrr_34065/08_2025/7yrr_34065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yrr_34065/08_2025/7yrr_34065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrr_34065/08_2025/7yrr_34065.map" model { file = "/net/cci-nas-00/data/ceres_data/7yrr_34065/08_2025/7yrr_34065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrr_34065/08_2025/7yrr_34065.cif" } resolution = 4.3 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 796 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 114 5.16 5 C 8520 2.51 5 N 2330 2.21 5 O 2565 1.98 5 H 11408 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24937 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 12029 Classifications: {'peptide': 799} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 47, 'TRANS': 751} Chain breaks: 20 Chain: "B" Number of atoms: 12242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 12242 Classifications: {'peptide': 810} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 47, 'TRANS': 762} Chain breaks: 13 Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 333 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Chain: "D" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 333 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Time building chain proxies: 4.85, per 1000 atoms: 0.19 Number of scatterers: 24937 At special positions: 0 Unit cell: (96.759, 127.358, 139.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 O 2565 8.00 N 2330 7.00 C 8520 6.00 H 11408 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.06 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.01 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.07 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.05 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.02 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.02 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.02 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.02 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.04 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.04 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.01 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=1.99 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.04 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.02 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.02 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.02 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.02 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.04 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 48 " distance=2.02 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 61 " distance=2.02 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 52 " 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: 2.05 Conformation dependent library (CDL) restraints added in 806.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 27 sheets defined 15.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.625A pdb=" N LYS A 17 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.325A pdb=" N ASP A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.736A pdb=" N LEU A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.492A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.526A pdb=" N TYR A 388 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.700A pdb=" N MET A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 removed outlier: 3.716A pdb=" N GLY A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 678 through 698 removed outlier: 4.246A pdb=" N GLU A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 696 " --> pdb=" O PHE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.609A pdb=" N LYS B 17 " --> pdb=" O GLN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.940A pdb=" N GLY B 149 " --> pdb=" O PRO B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.925A pdb=" N CYS B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 320 removed outlier: 4.247A pdb=" N LEU B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.113A pdb=" N PHE B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 372 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 372' Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.799A pdb=" N GLU B 428 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 429 " --> pdb=" O VAL B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 429' Processing helix chain 'B' and resid 512 through 516 removed outlier: 3.689A pdb=" N GLY B 515 " --> pdb=" O ASP B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 668 through 672 removed outlier: 4.171A pdb=" N ALA B 671 " --> pdb=" O PRO B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 removed outlier: 4.446A pdb=" N TYR B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing helix chain 'C' and resid 6 through 18 removed outlier: 3.614A pdb=" N VAL C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.571A pdb=" N TYR D 60 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS D 61 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 6.722A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.719A pdb=" N GLU A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 231 removed outlier: 5.880A pdb=" N TYR A 225 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N ASP A 248 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 393 removed outlier: 6.336A pdb=" N VAL A 392 " --> pdb=" O ALA A 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 465 through 467 removed outlier: 4.055A pdb=" N SER A 467 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.534A pdb=" N LYS A 600 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 614 through 618 Processing sheet with id=AB1, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.540A pdb=" N ALA A 793 " --> pdb=" O TYR A 769 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 812 through 813 Processing sheet with id=AB3, first strand: chain 'A' and resid 846 through 851 Processing sheet with id=AB4, first strand: chain 'A' and resid 869 through 870 Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.439A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 85 through 88 removed outlier: 7.789A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.572A pdb=" N GLU B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 230 through 231 Processing sheet with id=AB9, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AC1, first strand: chain 'B' and resid 310 through 311 Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC3, first strand: chain 'B' and resid 392 through 393 removed outlier: 6.322A pdb=" N VAL B 392 " --> pdb=" O ALA B 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AC5, first strand: chain 'B' and resid 587 through 590 Processing sheet with id=AC6, first strand: chain 'B' and resid 747 through 752 removed outlier: 3.600A pdb=" N SER B 750 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AC8, first strand: chain 'B' and resid 834 through 838 Processing sheet with id=AC9, first strand: chain 'B' and resid 869 through 870 189 hydrogen bonds defined for protein. 417 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: 5.86 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11408 1.03 - 1.23: 252 1.23 - 1.43: 5641 1.43 - 1.62: 7782 1.62 - 1.82: 144 Bond restraints: 25227 Sorted by residual: bond pdb=" C PRO A 543 " pdb=" O PRO A 543 " ideal model delta sigma weight residual 1.233 1.155 0.078 1.13e-02 7.83e+03 4.73e+01 bond pdb=" C PRO B 144 " pdb=" O PRO B 144 " ideal model delta sigma weight residual 1.240 1.173 0.067 1.12e-02 7.97e+03 3.63e+01 bond pdb=" C VAL B 426 " pdb=" O VAL B 426 " ideal model delta sigma weight residual 1.241 1.171 0.070 1.19e-02 7.06e+03 3.44e+01 bond pdb=" N ARG B 455 " pdb=" CA ARG B 455 " ideal model delta sigma weight residual 1.457 1.490 -0.033 6.40e-03 2.44e+04 2.67e+01 bond pdb=" C ILE B 615 " pdb=" O ILE B 615 " ideal model delta sigma weight residual 1.236 1.186 0.050 9.80e-03 1.04e+04 2.58e+01 ... (remaining 25222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 36628 2.16 - 4.32: 7115 4.32 - 6.48: 772 6.48 - 8.64: 77 8.64 - 10.80: 7 Bond angle restraints: 44599 Sorted by residual: angle pdb=" N PRO A 603 " pdb=" CA PRO A 603 " pdb=" C PRO A 603 " ideal model delta sigma weight residual 110.70 100.10 10.60 1.22e+00 6.72e-01 7.55e+01 angle pdb=" N PRO B 144 " pdb=" CA PRO B 144 " pdb=" C PRO B 144 " ideal model delta sigma weight residual 110.70 120.47 -9.77 1.22e+00 6.72e-01 6.42e+01 angle pdb=" N ASN B 694 " pdb=" CA ASN B 694 " pdb=" C ASN B 694 " ideal model delta sigma weight residual 112.94 102.31 10.63 1.41e+00 5.03e-01 5.69e+01 angle pdb=" N PHE B 692 " pdb=" CA PHE B 692 " pdb=" C PHE B 692 " ideal model delta sigma weight residual 113.23 104.26 8.97 1.24e+00 6.50e-01 5.23e+01 angle pdb=" N ILE B 106 " pdb=" CA ILE B 106 " pdb=" C ILE B 106 " ideal model delta sigma weight residual 112.43 105.88 6.55 9.20e-01 1.18e+00 5.08e+01 ... (remaining 44594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9713 17.99 - 35.97: 1300 35.97 - 53.96: 824 53.96 - 71.94: 324 71.94 - 89.93: 138 Dihedral angle restraints: 12299 sinusoidal: 6550 harmonic: 5749 Sorted by residual: dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 200 " pdb=" CB CYS A 200 " ideal model delta sinusoidal sigma weight residual 93.00 179.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS A 205 " pdb=" SG CYS A 205 " pdb=" SG CYS A 218 " pdb=" CB CYS A 218 " ideal model delta sinusoidal sigma weight residual -86.00 -167.21 81.21 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual -86.00 -5.76 -80.24 1 1.00e+01 1.00e-02 7.97e+01 ... (remaining 12296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1012 0.084 - 0.168: 738 0.168 - 0.252: 239 0.252 - 0.336: 25 0.336 - 0.420: 1 Chirality restraints: 2015 Sorted by residual: chirality pdb=" CA PHE B 695 " pdb=" N PHE B 695 " pdb=" C PHE B 695 " pdb=" CB PHE B 695 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ILE A 34 " pdb=" N ILE A 34 " pdb=" C ILE A 34 " pdb=" CB ILE A 34 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE A 491 " pdb=" CA ILE A 491 " pdb=" CG1 ILE A 491 " pdb=" CG2 ILE A 491 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 2012 not shown) Planarity restraints: 3773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 816 " 0.014 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CG ASN B 816 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN B 816 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 816 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 816 " -0.765 2.00e-02 2.50e+03 pdb="HD22 ASN B 816 " 0.765 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 168 " 0.020 2.00e-02 2.50e+03 4.42e-01 2.92e+03 pdb=" CG ASN A 168 " 0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN A 168 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 168 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 168 " 0.764 2.00e-02 2.50e+03 pdb="HD22 ASN A 168 " -0.765 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 520 " 0.027 2.00e-02 2.50e+03 4.42e-01 2.92e+03 pdb=" CG ASN A 520 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 520 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 520 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 520 " 0.765 2.00e-02 2.50e+03 pdb="HD22 ASN A 520 " -0.763 2.00e-02 2.50e+03 ... (remaining 3770 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.82: 24 1.82 - 2.51: 16852 2.51 - 3.21: 80862 3.21 - 3.90: 106235 3.90 - 4.60: 158835 Nonbonded interactions: 362808 Sorted by model distance: nonbonded pdb=" H LEU B 556 " pdb="HD21 LEU B 556 " model vdw 1.125 2.270 nonbonded pdb=" OE1 GLU A 204 " pdb=" HA GLU A 204 " model vdw 1.423 2.620 nonbonded pdb="HD23 LEU B 866 " pdb=" HZ PHE B 892 " model vdw 1.522 2.270 nonbonded pdb=" HB3 ASP B 586 " pdb=" HB3 ASN B 602 " model vdw 1.570 2.440 nonbonded pdb=" HA LEU A 256 " pdb="HD23 LEU A 256 " model vdw 1.570 2.440 ... (remaining 362803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 193 or (resid 194 and ( \ name N or name CA or name C or name O or name CB or name SG )) or resid 195 thro \ ugh 233 or resid 235 through 298 or (resid 299 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 300 through 384 or resid \ 387 through 574 or resid 576 through 605 or resid 607 through 897)) selection = (chain 'B' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O )) or resid 5 through 119 or resid 123 through 136 or resid 138 through \ 139 or resid 142 through 172 or (resid 173 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or \ name CZ or name OH )) or resid 175 through 197 or resid 199 through 396 or resid \ 398 through 422 or resid 424 through 481 or resid 484 through 488 or (resid 489 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name OD2)) or resid 491 through 498 or resid 500 through 528 or resid 530 throu \ gh 546 or resid 548 through 576 or (resid 577 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2)) or resid 578 through 61 \ 9 or resid 622 through 897)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.170 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.500 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4795 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 : 0.013 0.078 13853 Z= 0.976 Angle : 2.133 12.544 18758 Z= 1.509 Chirality : 0.112 0.420 2015 Planarity : 0.006 0.041 2425 Dihedral : 22.388 88.851 5145 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 5.56 % Allowed : 21.43 % Favored : 73.01 % Rotamer: Outliers : 26.25 % Allowed : 19.00 % Favored : 54.75 % Cbeta Deviations : 0.31 % 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: -5.95 (0.16), residues: 1619 helix: -4.05 (0.21), residues: 193 sheet: -4.35 (0.29), residues: 174 loop : -4.27 (0.14), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 44 TYR 0.042 0.005 TYR A 496 PHE 0.041 0.005 PHE A 892 TRP 0.027 0.005 TRP A 176 HIS 0.012 0.003 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.01309 (13819) covalent geometry : angle 2.12757 (18690) SS BOND : bond 0.01372 ( 34) SS BOND : angle 3.24716 ( 68) hydrogen bonds : bond 0.26392 ( 189) hydrogen bonds : angle 13.32293 ( 417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 395 poor density : 326 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6184 (mmt180) REVERT: A 255 ILE cc_start: 0.4429 (OUTLIER) cc_final: 0.4034 (pt) REVERT: A 257 SER cc_start: 0.2673 (OUTLIER) cc_final: 0.1893 (m) REVERT: A 279 SER cc_start: 0.6667 (OUTLIER) cc_final: 0.5864 (t) REVERT: A 333 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6514 (m-40) REVERT: A 375 LEU cc_start: 0.8765 (tp) cc_final: 0.8552 (tp) REVERT: A 455 ARG cc_start: 0.5081 (mmp-170) cc_final: 0.4555 (mtp-110) REVERT: A 493 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.5819 (t80) REVERT: A 556 LEU cc_start: 0.4270 (OUTLIER) cc_final: 0.3566 (mp) REVERT: A 558 MET cc_start: 0.3117 (pmm) cc_final: 0.2401 (ppp) REVERT: A 593 SER cc_start: 0.6451 (OUTLIER) cc_final: 0.5253 (m) REVERT: A 756 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: A 846 GLN cc_start: 0.4525 (OUTLIER) cc_final: 0.4048 (mm110) REVERT: B 144 PRO cc_start: 0.4878 (OUTLIER) cc_final: 0.4588 (Cg_endo) REVERT: B 156 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5518 (ptp) REVERT: B 199 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: B 257 SER cc_start: 0.4251 (OUTLIER) cc_final: 0.3813 (m) REVERT: B 264 GLU cc_start: 0.5146 (OUTLIER) cc_final: 0.4582 (pm20) REVERT: B 295 GLU cc_start: 0.6893 (mp0) cc_final: 0.6527 (mp0) REVERT: B 321 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.5435 (tm-30) REVERT: B 340 ILE cc_start: 0.5752 (OUTLIER) cc_final: 0.5500 (pt) REVERT: B 378 ILE cc_start: 0.6044 (mm) cc_final: 0.5689 (mm) REVERT: B 391 TYR cc_start: 0.3483 (OUTLIER) cc_final: 0.3237 (t80) REVERT: B 426 VAL cc_start: 0.6131 (OUTLIER) cc_final: 0.5814 (m) REVERT: B 468 THR cc_start: 0.8426 (p) cc_final: 0.8214 (p) REVERT: B 514 CYS cc_start: 0.5348 (OUTLIER) cc_final: 0.5049 (m) REVERT: B 542 LYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5637 (mmmt) REVERT: B 574 ILE cc_start: 0.5082 (OUTLIER) cc_final: 0.3744 (tt) REVERT: B 580 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7179 (m) REVERT: B 593 SER cc_start: 0.5375 (OUTLIER) cc_final: 0.4973 (t) REVERT: B 674 LYS cc_start: 0.3544 (OUTLIER) cc_final: 0.3343 (tppt) REVERT: B 701 PHE cc_start: 0.3350 (OUTLIER) cc_final: 0.2969 (p90) REVERT: C 54 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7075 (mp) REVERT: C 58 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5450 (pt0) REVERT: D 54 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7197 (mp) REVERT: D 58 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6294 (pt0) outliers start: 395 outliers final: 115 residues processed: 617 average time/residue: 0.2691 time to fit residues: 236.4528 Evaluate side-chains 368 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 223 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 400 GLN A 520 ASN A 680 GLN ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.186127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.168518 restraints weight = 90613.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.171119 restraints weight = 64677.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.172828 restraints weight = 42254.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.173484 restraints weight = 29712.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.173643 restraints weight = 25486.900| |-----------------------------------------------------------------------------| r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4626 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 13853 Z= 0.212 Angle : 0.866 9.856 18758 Z= 0.456 Chirality : 0.047 0.246 2015 Planarity : 0.008 0.148 2425 Dihedral : 6.042 29.695 1842 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 33.31 Ramachandran Plot: Outliers : 1.17 % Allowed : 18.59 % Favored : 80.23 % Rotamer: Outliers : 0.53 % Allowed : 4.25 % Favored : 95.22 % 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: -5.77 (0.16), residues: 1619 helix: -3.74 (0.22), residues: 218 sheet: -4.23 (0.27), residues: 203 loop : -4.13 (0.15), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 21 TYR 0.027 0.003 TYR B 688 PHE 0.035 0.003 PHE B 695 TRP 0.024 0.003 TRP A 822 HIS 0.013 0.003 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00495 (13819) covalent geometry : angle 0.84642 (18690) SS BOND : bond 0.00813 ( 34) SS BOND : angle 3.16756 ( 68) hydrogen bonds : bond 0.05876 ( 189) hydrogen bonds : angle 9.58700 ( 417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 267 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.0071 (pptt) cc_final: -0.0490 (pttt) REVERT: A 375 LEU cc_start: 0.8909 (tp) cc_final: 0.8445 (tt) REVERT: A 416 MET cc_start: -0.0532 (mmp) cc_final: -0.0838 (mmp) REVERT: A 521 MET cc_start: 0.4300 (tpt) cc_final: 0.3404 (ttt) REVERT: B 80 LYS cc_start: 0.4255 (mttm) cc_final: 0.3706 (mttt) REVERT: B 213 ASP cc_start: 0.5964 (t0) cc_final: 0.5490 (t0) REVERT: B 375 LEU cc_start: 0.8643 (tp) cc_final: 0.8255 (tp) REVERT: B 693 GLU cc_start: 0.5312 (mp0) cc_final: 0.5040 (mp0) REVERT: D 15 GLN cc_start: 0.4575 (tm-30) cc_final: 0.2913 (mm-40) REVERT: D 58 GLU cc_start: 0.6497 (pt0) cc_final: 0.5702 (tm-30) outliers start: 8 outliers final: 2 residues processed: 274 average time/residue: 0.2493 time to fit residues: 99.9708 Evaluate side-chains 206 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 364 HIS ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 451 ASN A 697 HIS ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN B 383 GLN B 397 ASN B 399 GLN B 451 ASN ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.178542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.157275 restraints weight = 95823.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.160348 restraints weight = 59328.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.161590 restraints weight = 40451.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.162004 restraints weight = 33330.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.162299 restraints weight = 30458.218| |-----------------------------------------------------------------------------| r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5156 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 13853 Z= 0.233 Angle : 0.824 10.114 18758 Z= 0.431 Chirality : 0.047 0.268 2015 Planarity : 0.007 0.105 2425 Dihedral : 6.015 35.021 1842 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 32.52 Ramachandran Plot: Outliers : 1.05 % Allowed : 20.01 % Favored : 78.94 % Rotamer: Outliers : 0.33 % Allowed : 3.85 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -5.55 (0.17), residues: 1619 helix: -3.63 (0.23), residues: 215 sheet: -4.40 (0.26), residues: 220 loop : -3.86 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 689 TYR 0.035 0.002 TYR A 858 PHE 0.057 0.003 PHE A 701 TRP 0.023 0.003 TRP A 402 HIS 0.009 0.002 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00534 (13819) covalent geometry : angle 0.80844 (18690) SS BOND : bond 0.00585 ( 34) SS BOND : angle 2.74543 ( 68) hydrogen bonds : bond 0.05166 ( 189) hydrogen bonds : angle 8.95628 ( 417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 227 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.0048 (pptt) cc_final: -0.0434 (pttt) REVERT: A 416 MET cc_start: -0.0656 (mmp) cc_final: -0.0962 (mmp) REVERT: A 521 MET cc_start: 0.4165 (tpt) cc_final: 0.3762 (ttt) REVERT: B 213 ASP cc_start: 0.6686 (t0) cc_final: 0.6314 (t0) REVERT: B 375 LEU cc_start: 0.8730 (tp) cc_final: 0.8473 (tp) REVERT: B 471 SER cc_start: 0.8188 (t) cc_final: 0.7959 (m) REVERT: D 20 ASP cc_start: 0.7632 (m-30) cc_final: 0.7423 (m-30) outliers start: 5 outliers final: 2 residues processed: 229 average time/residue: 0.2524 time to fit residues: 84.7350 Evaluate side-chains 192 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 73 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 158 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 374 ASN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS B 399 GLN ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.178697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.156186 restraints weight = 101610.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.158620 restraints weight = 71107.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.159927 restraints weight = 49741.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.160817 restraints weight = 40783.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.161037 restraints weight = 38548.304| |-----------------------------------------------------------------------------| r_work (final): 0.4564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5243 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13853 Z= 0.177 Angle : 0.701 6.985 18758 Z= 0.368 Chirality : 0.044 0.157 2015 Planarity : 0.006 0.123 2425 Dihedral : 5.797 36.531 1842 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 28.15 Ramachandran Plot: Outliers : 0.99 % Allowed : 17.85 % Favored : 81.16 % Rotamer: Outliers : 0.20 % Allowed : 3.19 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -5.24 (0.17), residues: 1619 helix: -3.19 (0.27), residues: 205 sheet: -4.22 (0.26), residues: 234 loop : -3.66 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 689 TYR 0.022 0.002 TYR D 60 PHE 0.038 0.002 PHE A 701 TRP 0.027 0.002 TRP B 79 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00410 (13819) covalent geometry : angle 0.68913 (18690) SS BOND : bond 0.00549 ( 34) SS BOND : angle 2.22151 ( 68) hydrogen bonds : bond 0.04514 ( 189) hydrogen bonds : angle 8.39234 ( 417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 214 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.0093 (pptt) cc_final: -0.0411 (pttt) REVERT: A 348 MET cc_start: 0.6132 (mmm) cc_final: 0.5725 (mmt) REVERT: A 416 MET cc_start: -0.0748 (mmp) cc_final: -0.0966 (mmp) REVERT: A 521 MET cc_start: 0.4374 (tpt) cc_final: 0.4044 (ttt) REVERT: B 248 ASP cc_start: 0.7634 (p0) cc_final: 0.7413 (p0) REVERT: B 367 VAL cc_start: 0.6901 (p) cc_final: 0.6437 (p) REVERT: B 399 GLN cc_start: 0.5238 (pt0) cc_final: 0.5000 (pt0) REVERT: B 471 SER cc_start: 0.8116 (t) cc_final: 0.7853 (m) REVERT: B 601 TRP cc_start: 0.6277 (p90) cc_final: 0.5979 (p90) REVERT: B 693 GLU cc_start: 0.6349 (mp0) cc_final: 0.6148 (mp0) REVERT: D 20 ASP cc_start: 0.7544 (m-30) cc_final: 0.7208 (m-30) REVERT: D 50 ARG cc_start: 0.6434 (mtp-110) cc_final: 0.6141 (mtm110) outliers start: 3 outliers final: 2 residues processed: 215 average time/residue: 0.2670 time to fit residues: 83.8091 Evaluate side-chains 186 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 156 optimal weight: 30.0000 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 374 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN B 169 ASN B 223 HIS B 399 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.174908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.154445 restraints weight = 97534.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.156566 restraints weight = 64310.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.158104 restraints weight = 45484.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.158333 restraints weight = 35052.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.158814 restraints weight = 33790.337| |-----------------------------------------------------------------------------| r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5324 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13853 Z= 0.223 Angle : 0.748 8.099 18758 Z= 0.394 Chirality : 0.045 0.255 2015 Planarity : 0.006 0.097 2425 Dihedral : 5.916 38.130 1842 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 32.03 Ramachandran Plot: Outliers : 0.99 % Allowed : 19.95 % Favored : 79.06 % Rotamer: Outliers : 0.20 % Allowed : 2.99 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -5.12 (0.18), residues: 1619 helix: -3.04 (0.28), residues: 194 sheet: -4.28 (0.27), residues: 228 loop : -3.56 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 21 TYR 0.024 0.002 TYR D 60 PHE 0.030 0.002 PHE A 701 TRP 0.026 0.002 TRP A 402 HIS 0.009 0.002 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00497 (13819) covalent geometry : angle 0.73071 (18690) SS BOND : bond 0.00581 ( 34) SS BOND : angle 2.72176 ( 68) hydrogen bonds : bond 0.04510 ( 189) hydrogen bonds : angle 8.25952 ( 417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.0222 (pptt) cc_final: -0.0272 (pttt) REVERT: A 348 MET cc_start: 0.6151 (mmm) cc_final: 0.5627 (mmt) REVERT: A 468 THR cc_start: 0.8321 (p) cc_final: 0.8115 (t) REVERT: B 213 ASP cc_start: 0.6353 (t0) cc_final: 0.6021 (t0) REVERT: B 375 LEU cc_start: 0.8690 (tp) cc_final: 0.8329 (tp) REVERT: B 471 SER cc_start: 0.8282 (t) cc_final: 0.7992 (m) REVERT: D 20 ASP cc_start: 0.7683 (m-30) cc_final: 0.7366 (m-30) REVERT: D 50 ARG cc_start: 0.6504 (mtp-110) cc_final: 0.6128 (mtm110) outliers start: 3 outliers final: 2 residues processed: 204 average time/residue: 0.2493 time to fit residues: 75.4240 Evaluate side-chains 176 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 163 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN A 694 ASN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN B 630 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.176345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.154722 restraints weight = 97879.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.156627 restraints weight = 66658.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.158515 restraints weight = 48675.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.159369 restraints weight = 34812.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.159748 restraints weight = 30697.504| |-----------------------------------------------------------------------------| r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5288 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13853 Z= 0.159 Angle : 0.677 7.588 18758 Z= 0.352 Chirality : 0.043 0.155 2015 Planarity : 0.006 0.101 2425 Dihedral : 5.811 36.424 1842 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.93 % Allowed : 16.99 % Favored : 82.09 % Rotamer: Outliers : 0.20 % Allowed : 1.66 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.88 (0.18), residues: 1619 helix: -2.74 (0.30), residues: 199 sheet: -4.03 (0.28), residues: 208 loop : -3.47 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 336 TYR 0.022 0.002 TYR A 173 PHE 0.022 0.002 PHE A 701 TRP 0.024 0.002 TRP A 402 HIS 0.010 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00364 (13819) covalent geometry : angle 0.66162 (18690) SS BOND : bond 0.00479 ( 34) SS BOND : angle 2.44806 ( 68) hydrogen bonds : bond 0.04075 ( 189) hydrogen bonds : angle 7.86592 ( 417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.0265 (pptt) cc_final: -0.0304 (pttt) REVERT: A 339 ASN cc_start: 0.5115 (m-40) cc_final: 0.4533 (t0) REVERT: A 348 MET cc_start: 0.6036 (mmm) cc_final: 0.5481 (mmt) REVERT: B 248 ASP cc_start: 0.7517 (p0) cc_final: 0.7300 (p0) REVERT: B 367 VAL cc_start: 0.7002 (p) cc_final: 0.6436 (p) REVERT: B 471 SER cc_start: 0.8118 (t) cc_final: 0.7832 (m) REVERT: D 20 ASP cc_start: 0.7643 (m-30) cc_final: 0.7285 (m-30) REVERT: D 50 ARG cc_start: 0.6358 (mtp-110) cc_final: 0.6136 (mtm110) outliers start: 3 outliers final: 2 residues processed: 212 average time/residue: 0.2549 time to fit residues: 79.7223 Evaluate side-chains 176 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 86 optimal weight: 0.0970 chunk 163 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 ASN B 399 GLN ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN B 630 HIS ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.177605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.157504 restraints weight = 104060.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.159698 restraints weight = 71787.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.161211 restraints weight = 50946.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.162151 restraints weight = 38134.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.162033 restraints weight = 35860.214| |-----------------------------------------------------------------------------| r_work (final): 0.4575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5164 moved from start: 0.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13853 Z= 0.120 Angle : 0.623 6.620 18758 Z= 0.323 Chirality : 0.043 0.232 2015 Planarity : 0.005 0.060 2425 Dihedral : 5.497 32.877 1842 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.86 % Allowed : 17.11 % Favored : 82.03 % Rotamer: Outliers : 0.27 % Allowed : 1.20 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.64 (0.19), residues: 1619 helix: -2.29 (0.33), residues: 199 sheet: -3.88 (0.28), residues: 206 loop : -3.35 (0.16), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 689 TYR 0.013 0.001 TYR B 224 PHE 0.018 0.002 PHE A 371 TRP 0.024 0.002 TRP A 402 HIS 0.005 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00286 (13819) covalent geometry : angle 0.61249 (18690) SS BOND : bond 0.00335 ( 34) SS BOND : angle 1.98124 ( 68) hydrogen bonds : bond 0.03646 ( 189) hydrogen bonds : angle 7.50257 ( 417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 208 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.0306 (pptt) cc_final: -0.0015 (pttt) REVERT: A 311 ILE cc_start: 0.6519 (mm) cc_final: 0.6002 (pt) REVERT: A 339 ASN cc_start: 0.5063 (m-40) cc_final: 0.4619 (t0) REVERT: A 348 MET cc_start: 0.5989 (mmm) cc_final: 0.5461 (mmt) REVERT: A 424 LEU cc_start: 0.5937 (tp) cc_final: 0.5639 (tp) REVERT: B 248 ASP cc_start: 0.7289 (p0) cc_final: 0.7089 (p0) REVERT: D 20 ASP cc_start: 0.7437 (m-30) cc_final: 0.7055 (m-30) outliers start: 4 outliers final: 3 residues processed: 210 average time/residue: 0.2474 time to fit residues: 76.9461 Evaluate side-chains 185 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 374 ASN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.174840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.154699 restraints weight = 98290.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.156538 restraints weight = 67661.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.157145 restraints weight = 46478.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.157284 restraints weight = 44098.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.157441 restraints weight = 40794.216| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5346 moved from start: 0.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13853 Z= 0.185 Angle : 0.680 6.805 18758 Z= 0.355 Chirality : 0.044 0.226 2015 Planarity : 0.006 0.080 2425 Dihedral : 5.633 35.810 1842 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.74 % Allowed : 19.39 % Favored : 79.86 % Rotamer: Outliers : 0.13 % Allowed : 1.20 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.64 (0.18), residues: 1619 helix: -2.39 (0.32), residues: 199 sheet: -3.74 (0.30), residues: 199 loop : -3.37 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 689 TYR 0.016 0.002 TYR B 224 PHE 0.021 0.002 PHE A 701 TRP 0.027 0.002 TRP A 402 HIS 0.009 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00414 (13819) covalent geometry : angle 0.66821 (18690) SS BOND : bond 0.00407 ( 34) SS BOND : angle 2.20160 ( 68) hydrogen bonds : bond 0.04052 ( 189) hydrogen bonds : angle 7.60200 ( 417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.0755 (pptt) cc_final: 0.0275 (pttt) REVERT: A 339 ASN cc_start: 0.5244 (m-40) cc_final: 0.4633 (t0) REVERT: A 348 MET cc_start: 0.6091 (mmm) cc_final: 0.5686 (mmm) REVERT: A 424 LEU cc_start: 0.5779 (tp) cc_final: 0.5546 (tp) REVERT: A 773 ILE cc_start: 0.9062 (tt) cc_final: 0.8705 (mp) REVERT: B 248 ASP cc_start: 0.7447 (p0) cc_final: 0.7171 (p0) REVERT: B 366 LEU cc_start: 0.7189 (mt) cc_final: 0.6863 (mp) REVERT: B 367 VAL cc_start: 0.7112 (p) cc_final: 0.6228 (p) REVERT: D 20 ASP cc_start: 0.7785 (m-30) cc_final: 0.7333 (m-30) outliers start: 2 outliers final: 2 residues processed: 203 average time/residue: 0.2516 time to fit residues: 75.5961 Evaluate side-chains 173 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.176063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.155770 restraints weight = 97272.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.157963 restraints weight = 61350.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.159684 restraints weight = 43821.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.160437 restraints weight = 32955.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.161005 restraints weight = 28064.350| |-----------------------------------------------------------------------------| r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5230 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13853 Z= 0.144 Angle : 0.648 7.651 18758 Z= 0.336 Chirality : 0.043 0.182 2015 Planarity : 0.005 0.072 2425 Dihedral : 5.633 33.518 1842 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.74 % Allowed : 17.73 % Favored : 81.53 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.53 (0.19), residues: 1619 helix: -2.23 (0.33), residues: 198 sheet: -3.65 (0.30), residues: 194 loop : -3.32 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 689 TYR 0.023 0.001 TYR B 547 PHE 0.018 0.002 PHE B 493 TRP 0.027 0.002 TRP A 402 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00335 (13819) covalent geometry : angle 0.63409 (18690) SS BOND : bond 0.00345 ( 34) SS BOND : angle 2.33865 ( 68) hydrogen bonds : bond 0.03700 ( 189) hydrogen bonds : angle 7.42085 ( 417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.0386 (pptt) cc_final: -0.0002 (pttt) REVERT: A 339 ASN cc_start: 0.4979 (m-40) cc_final: 0.4563 (t0) REVERT: A 348 MET cc_start: 0.5995 (mmm) cc_final: 0.5689 (mmm) REVERT: A 409 LEU cc_start: 0.6672 (mp) cc_final: 0.6366 (mp) REVERT: A 424 LEU cc_start: 0.5941 (tp) cc_final: 0.5685 (tp) REVERT: A 773 ILE cc_start: 0.9091 (tt) cc_final: 0.8672 (mp) REVERT: B 248 ASP cc_start: 0.7412 (p0) cc_final: 0.7189 (p0) REVERT: B 366 LEU cc_start: 0.7216 (mt) cc_final: 0.6901 (mp) REVERT: D 20 ASP cc_start: 0.7727 (m-30) cc_final: 0.7291 (m-30) outliers start: 2 outliers final: 2 residues processed: 204 average time/residue: 0.2542 time to fit residues: 76.4280 Evaluate side-chains 174 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 4.9990 chunk 125 optimal weight: 0.0570 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 77 optimal weight: 40.0000 chunk 154 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.175832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.154659 restraints weight = 98254.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.157050 restraints weight = 61392.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.158601 restraints weight = 42521.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.159457 restraints weight = 33063.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.160612 restraints weight = 28412.704| |-----------------------------------------------------------------------------| r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5206 moved from start: 0.7639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13853 Z= 0.143 Angle : 0.643 7.574 18758 Z= 0.333 Chirality : 0.043 0.175 2015 Planarity : 0.005 0.064 2425 Dihedral : 5.595 33.139 1842 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.74 % Allowed : 18.78 % Favored : 80.48 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.47 (0.19), residues: 1619 helix: -2.25 (0.33), residues: 200 sheet: -3.50 (0.33), residues: 173 loop : -3.30 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 336 TYR 0.027 0.002 TYR B 547 PHE 0.018 0.002 PHE B 502 TRP 0.026 0.002 TRP A 402 HIS 0.008 0.002 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00333 (13819) covalent geometry : angle 0.63158 (18690) SS BOND : bond 0.00378 ( 34) SS BOND : angle 2.13485 ( 68) hydrogen bonds : bond 0.03671 ( 189) hydrogen bonds : angle 7.30486 ( 417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.0228 (pptt) cc_final: -0.0079 (pttt) REVERT: A 339 ASN cc_start: 0.5119 (m-40) cc_final: 0.4494 (t0) REVERT: A 348 MET cc_start: 0.6004 (mmm) cc_final: 0.5670 (mmm) REVERT: A 773 ILE cc_start: 0.9091 (tt) cc_final: 0.8698 (mp) REVERT: B 366 LEU cc_start: 0.7150 (mt) cc_final: 0.6869 (mp) REVERT: B 367 VAL cc_start: 0.6824 (p) cc_final: 0.6146 (p) outliers start: 2 outliers final: 2 residues processed: 200 average time/residue: 0.2457 time to fit residues: 72.9471 Evaluate side-chains 173 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6983 > 50: distance: 78 - 263: 12.300 distance: 81 - 260: 3.730 distance: 111 - 224: 33.274 distance: 114 - 221: 22.265 distance: 136 - 194: 35.369 distance: 139 - 191: 35.243 distance: 183 - 191: 35.293 distance: 191 - 192: 23.264 distance: 191 - 197: 58.060 distance: 192 - 193: 39.295 distance: 192 - 195: 59.399 distance: 192 - 198: 41.214 distance: 193 - 194: 49.029 distance: 193 - 202: 29.073 distance: 195 - 196: 48.008 distance: 195 - 199: 20.158 distance: 195 - 200: 25.414 distance: 196 - 201: 23.623 distance: 202 - 203: 24.363 distance: 202 - 210: 39.712 distance: 203 - 204: 42.860 distance: 203 - 206: 18.356 distance: 203 - 211: 47.955 distance: 204 - 205: 43.248 distance: 204 - 221: 44.327 distance: 206 - 207: 24.365 distance: 206 - 208: 13.839 distance: 206 - 212: 42.062 distance: 207 - 209: 23.255 distance: 207 - 213: 24.492 distance: 207 - 214: 44.008 distance: 208 - 215: 30.293 distance: 208 - 216: 14.705 distance: 208 - 217: 27.568 distance: 209 - 218: 8.240 distance: 209 - 219: 36.046 distance: 209 - 220: 53.252 distance: 221 - 222: 11.324 distance: 221 - 232: 41.626 distance: 222 - 223: 42.017 distance: 222 - 225: 31.183 distance: 222 - 233: 41.043 distance: 223 - 224: 29.977 distance: 223 - 241: 29.266 distance: 225 - 226: 17.374 distance: 225 - 234: 14.571 distance: 225 - 235: 13.242 distance: 226 - 227: 37.543 distance: 226 - 228: 8.006 distance: 227 - 229: 26.727 distance: 227 - 236: 28.148 distance: 228 - 230: 10.139 distance: 228 - 237: 6.822 distance: 229 - 231: 13.313 distance: 229 - 238: 12.124 distance: 230 - 231: 7.681 distance: 230 - 239: 4.518 distance: 231 - 240: 7.622 distance: 241 - 242: 40.435 distance: 241 - 249: 31.128 distance: 241 - 502: 33.639 distance: 242 - 243: 14.998 distance: 242 - 245: 20.067 distance: 242 - 250: 30.822 distance: 243 - 244: 30.359 distance: 243 - 260: 21.665 distance: 244 - 499: 26.418 distance: 245 - 246: 20.120 distance: 245 - 251: 24.849 distance: 245 - 252: 54.296 distance: 246 - 247: 17.636 distance: 246 - 248: 26.757 distance: 246 - 253: 22.617 distance: 247 - 254: 21.102 distance: 247 - 255: 37.452 distance: 247 - 256: 35.076 distance: 248 - 257: 24.640 distance: 248 - 258: 26.362 distance: 248 - 259: 14.960 distance: 260 - 261: 19.955 distance: 260 - 269: 31.767 distance: 261 - 262: 34.480 distance: 261 - 264: 24.137 distance: 261 - 270: 36.836 distance: 262 - 263: 36.497 distance: 262 - 282: 52.273 distance: 264 - 265: 23.024 distance: 264 - 271: 33.966 distance: 264 - 272: 22.313 distance: 265 - 266: 15.835 distance: 265 - 273: 28.762 distance: 265 - 274: 17.040 distance: 266 - 267: 19.636 distance: 266 - 275: 13.430 distance: 266 - 276: 12.452 distance: 267 - 268: 41.448 distance: 267 - 277: 35.926 distance: 267 - 278: 42.449 distance: 268 - 279: 21.384 distance: 268 - 280: 25.302 distance: 268 - 281: 29.367 distance: 282 - 283: 32.258 distance: 282 - 296: 51.586 distance: 283 - 284: 10.625 distance: 283 - 286: 20.370 distance: 283 - 297: 14.785 distance: 284 - 285: 51.952 distance: 284 - 306: 19.605 distance: 286 - 287: 25.354 distance: 286 - 298: 31.444 distance: 286 - 299: 13.093 distance: 287 - 288: 18.963 distance: 287 - 289: 13.058 distance: 288 - 290: 20.756 distance: 288 - 300: 3.736 distance: 289 - 291: 15.147 distance: 289 - 292: 14.267 distance: 290 - 291: 6.400 distance: 291 - 293: 3.262 distance: 292 - 294: 6.475 distance: 292 - 302: 8.720 distance: 293 - 295: 4.989 distance: 293 - 303: 4.709 distance: 294 - 295: 6.996 distance: 294 - 304: 7.182 distance: 295 - 305: 7.018 distance: 306 - 307: 49.368 distance: 306 - 312: 18.326 distance: 307 - 308: 39.384 distance: 307 - 310: 20.915 distance: 307 - 313: 12.515 distance: 308 - 309: 14.648 distance: 308 - 320: 3.563 distance: 310 - 311: 46.291 distance: 310 - 314: 15.208 distance: 310 - 315: 23.668 distance: 311 - 312: 33.800 distance: 311 - 316: 21.144 distance: 311 - 317: 21.000 distance: 312 - 318: 30.953 distance: 312 - 319: 40.081 distance: 320 - 321: 29.193 distance: 320 - 329: 53.369 distance: 321 - 322: 26.159 distance: 321 - 324: 30.450 distance: 321 - 330: 12.807 distance: 322 - 323: 19.406 distance: 322 - 335: 23.737 distance: 324 - 325: 52.849 distance: 324 - 331: 39.699 distance: 324 - 332: 13.344 distance: 325 - 326: 3.163 distance: 325 - 333: 41.670 distance: 325 - 334: 9.418 distance: 326 - 327: 52.599 distance: 326 - 328: 18.245 distance: 335 - 336: 36.956 distance: 335 - 341: 41.825 distance: 336 - 337: 45.161 distance: 336 - 339: 39.505 distance: 336 - 342: 53.769 distance: 337 - 338: 40.853 distance: 337 - 349: 39.665 distance: 339 - 343: 61.591 distance: 339 - 344: 56.117 distance: 340 - 341: 41.106 distance: 340 - 345: 55.680 distance: 340 - 346: 67.928 distance: 341 - 347: 6.080 distance: 341 - 348: 28.804 distance: 349 - 350: 20.830 distance: 349 - 358: 3.555 distance: 350 - 351: 42.907 distance: 350 - 353: 28.686 distance: 350 - 359: 29.043 distance: 351 - 352: 22.363 distance: 351 - 364: 27.859 distance: 353 - 354: 22.587 distance: 353 - 360: 32.765 distance: 353 - 361: 26.081 distance: 354 - 355: 60.267 distance: 354 - 362: 17.325 distance: 354 - 363: 45.886 distance: 355 - 356: 43.264 distance: 355 - 357: 17.963