Starting phenix.real_space_refine on Wed Feb 4 19:12:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vx1_43606/02_2026/8vx1_43606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vx1_43606/02_2026/8vx1_43606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vx1_43606/02_2026/8vx1_43606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vx1_43606/02_2026/8vx1_43606.map" model { file = "/net/cci-nas-00/data/ceres_data/8vx1_43606/02_2026/8vx1_43606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vx1_43606/02_2026/8vx1_43606.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 6213 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 P 41 5.49 5 S 34 5.16 5 C 4558 2.51 5 N 1285 2.21 5 O 1456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7374 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6520 Classifications: {'peptide': 861} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 98} Link IDs: {'PTRANS': 34, 'TRANS': 826} Chain breaks: 1 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 23, 'GLN:plan1': 13, 'ARG:plan': 11, 'HIS:plan': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 261 Chain: "C" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 518 Inner-chain residues flagged as termini: ['pdbres=" DA C 10 "'] Classifications: {'DNA': 27} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 26} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {' DT:plan': 2, ' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 336 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.73, per 1000 atoms: 0.23 Number of scatterers: 7374 At special positions: 0 Unit cell: (76.44, 105.84, 114.24, 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 34 16.00 P 41 15.00 O 1456 8.00 N 1285 7.00 C 4558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 165.8 milliseconds 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1630 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 53.4% alpha, 9.1% beta 6 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 61 through 82 removed outlier: 3.560A pdb=" N LYS A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.845A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 4.029A pdb=" N LEU A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 removed outlier: 3.777A pdb=" N PHE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 6.116A pdb=" N SER A 211 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 237 through 254 removed outlier: 4.505A pdb=" N THR A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 282 Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.511A pdb=" N LEU A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 removed outlier: 3.637A pdb=" N ARG A 341 " --> pdb=" O ILE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.626A pdb=" N ASP A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.818A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 431 through 456 removed outlier: 3.637A pdb=" N ALA A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Proline residue: A 446 - end of helix removed outlier: 3.642A pdb=" N GLN A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.570A pdb=" N VAL A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.513A pdb=" N GLN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.878A pdb=" N SER A 518 " --> pdb=" O MET A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.678A pdb=" N VAL A 533 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 560 removed outlier: 3.971A pdb=" N THR A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 559 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 560' Processing helix chain 'A' and resid 594 through 603 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.692A pdb=" N LYS A 646 " --> pdb=" O CYS A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.524A pdb=" N ARG A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.911A pdb=" N HIS A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 714 removed outlier: 3.557A pdb=" N MET A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 Processing helix chain 'A' and resid 740 through 752 removed outlier: 3.649A pdb=" N LYS A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 775 removed outlier: 4.169A pdb=" N VAL A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 774 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 789 through 811 removed outlier: 3.672A pdb=" N GLY A 801 " --> pdb=" O HIS A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 841 removed outlier: 3.598A pdb=" N ILE A 833 " --> pdb=" O ASN A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 879 removed outlier: 3.707A pdb=" N VAL A 878 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU A 879 " --> pdb=" O VAL A 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 875 through 879' Processing helix chain 'A' and resid 908 through 915 removed outlier: 3.595A pdb=" N LEU A 912 " --> pdb=" O SER A 908 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 914 " --> pdb=" O TYR A 910 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 915 " --> pdb=" O CYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 965 removed outlier: 3.507A pdb=" N LEU A 947 " --> pdb=" O ARG A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 988 Processing sheet with id=AA1, first strand: chain 'A' and resid 299 through 301 removed outlier: 3.842A pdb=" N THR A 313 " --> pdb=" O GLN A 295 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP A 336 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 228 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER A 368 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 230 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 398 removed outlier: 5.935A pdb=" N VAL A 396 " --> pdb=" O CYS A 613 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N HIS A 615 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR A 398 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 566 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N TYR A 614 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 568 " --> pdb=" O TYR A 614 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA A 492 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 493 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA A 552 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL A 495 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 551 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 577 Processing sheet with id=AA4, first strand: chain 'A' and resid 845 through 847 Processing sheet with id=AA5, first strand: chain 'A' and resid 850 through 851 removed outlier: 3.506A pdb=" N ASN A 851 " --> pdb=" O MET A 858 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET A 858 " --> pdb=" O ASN A 851 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 861 through 863 removed outlier: 3.888A pdb=" N VAL A 861 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LEU A 901 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 870 " --> pdb=" O LEU A 901 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 921 314 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1994 1.33 - 1.45: 1394 1.45 - 1.57: 4082 1.57 - 1.69: 81 1.69 - 1.81: 53 Bond restraints: 7604 Sorted by residual: bond pdb=" C ASN A 554 " pdb=" N ILE A 555 " ideal model delta sigma weight residual 1.335 1.319 0.015 1.20e-02 6.94e+03 1.66e+00 bond pdb=" N ASN A 554 " pdb=" CA ASN A 554 " ideal model delta sigma weight residual 1.460 1.487 -0.026 2.12e-02 2.22e+03 1.54e+00 bond pdb=" CA ILE A 848 " pdb=" C ILE A 848 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.27e-02 6.20e+03 8.22e-01 bond pdb=" CG ARG A 977 " pdb=" CD ARG A 977 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.54e-01 bond pdb=" CB ARG A 977 " pdb=" CG ARG A 977 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.79e-01 ... (remaining 7599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 10422 2.16 - 4.33: 88 4.33 - 6.49: 8 6.49 - 8.66: 2 8.66 - 10.82: 2 Bond angle restraints: 10522 Sorted by residual: angle pdb=" CG1 ILE A 848 " pdb=" CB ILE A 848 " pdb=" CG2 ILE A 848 " ideal model delta sigma weight residual 110.70 99.88 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA LEU A 679 " pdb=" CB LEU A 679 " pdb=" CG LEU A 679 " ideal model delta sigma weight residual 116.30 126.25 -9.95 3.50e+00 8.16e-02 8.08e+00 angle pdb=" CA ILE A 848 " pdb=" CB ILE A 848 " pdb=" CG2 ILE A 848 " ideal model delta sigma weight residual 110.50 115.09 -4.59 1.70e+00 3.46e-01 7.28e+00 angle pdb=" C ILE A 848 " pdb=" CA ILE A 848 " pdb=" CB ILE A 848 " ideal model delta sigma weight residual 111.29 115.57 -4.28 1.64e+00 3.72e-01 6.80e+00 angle pdb=" CA LEU A 355 " pdb=" CB LEU A 355 " pdb=" CG LEU A 355 " ideal model delta sigma weight residual 116.30 124.71 -8.41 3.50e+00 8.16e-02 5.78e+00 ... (remaining 10517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3598 17.63 - 35.26: 540 35.26 - 52.90: 212 52.90 - 70.53: 61 70.53 - 88.16: 7 Dihedral angle restraints: 4418 sinusoidal: 1901 harmonic: 2517 Sorted by residual: dihedral pdb=" CA ASP A 361 " pdb=" CB ASP A 361 " pdb=" CG ASP A 361 " pdb=" OD1 ASP A 361 " ideal model delta sinusoidal sigma weight residual -30.00 -89.72 59.72 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" N LYS A 517 " pdb=" CA LYS A 517 " pdb=" CB LYS A 517 " pdb=" CG LYS A 517 " ideal model delta sinusoidal sigma weight residual -180.00 -120.78 -59.22 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 918 " pdb=" CB ASP A 918 " pdb=" CG ASP A 918 " pdb=" OD1 ASP A 918 " ideal model delta sinusoidal sigma weight residual -30.00 -82.68 52.68 1 2.00e+01 2.50e-03 9.45e+00 ... (remaining 4415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 987 0.043 - 0.087: 171 0.087 - 0.130: 63 0.130 - 0.173: 0 0.173 - 0.216: 1 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CB ILE A 848 " pdb=" CA ILE A 848 " pdb=" CG1 ILE A 848 " pdb=" CG2 ILE A 848 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A 936 " pdb=" N ILE A 936 " pdb=" C ILE A 936 " pdb=" CB ILE A 936 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE A 551 " pdb=" N ILE A 551 " pdb=" C ILE A 551 " pdb=" CB ILE A 551 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1219 not shown) Planarity restraints: 1196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 689 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 690 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 690 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 690 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 354 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.55e+00 pdb=" CG ASP A 354 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP A 354 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 354 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 848 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C ILE A 848 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE A 848 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG A 849 " -0.007 2.00e-02 2.50e+03 ... (remaining 1193 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1720 2.79 - 3.32: 6718 3.32 - 3.85: 11634 3.85 - 4.37: 13287 4.37 - 4.90: 22849 Nonbonded interactions: 56208 Sorted by model distance: nonbonded pdb=" OG1 THR A 392 " pdb=" O GLY A 606 " model vdw 2.267 3.040 nonbonded pdb=" N1 DG C 6 " pdb=" O6 DG C 11 " model vdw 2.365 3.120 nonbonded pdb=" O ASN A 430 " pdb=" N GLN A 432 " model vdw 2.368 3.120 nonbonded pdb=" OG SER A 594 " pdb=" OD1 ASN A 597 " model vdw 2.373 3.040 nonbonded pdb=" N ASP A 324 " pdb=" OD1 ASP A 324 " model vdw 2.399 3.120 ... (remaining 56203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7604 Z= 0.097 Angle : 0.497 10.821 10522 Z= 0.259 Chirality : 0.037 0.216 1222 Planarity : 0.003 0.038 1196 Dihedral : 19.915 88.159 2788 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.65 % Favored : 92.88 % Rotamer: Outliers : 0.30 % Allowed : 30.19 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.30), residues: 857 helix: 1.07 (0.25), residues: 417 sheet: 0.67 (0.55), residues: 119 loop : -1.57 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 943 TYR 0.006 0.001 TYR A 842 PHE 0.017 0.001 PHE A 729 TRP 0.007 0.001 TRP A 887 HIS 0.002 0.000 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 7604) covalent geometry : angle 0.49748 (10522) hydrogen bonds : bond 0.27530 ( 326) hydrogen bonds : angle 6.29132 ( 906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.275 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.0684 time to fit residues: 7.1263 Evaluate side-chains 57 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS A 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.060772 restraints weight = 17326.289| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.16 r_work: 0.2694 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7604 Z= 0.128 Angle : 0.524 9.875 10522 Z= 0.279 Chirality : 0.039 0.253 1222 Planarity : 0.003 0.036 1196 Dihedral : 18.966 88.132 1330 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.18 % Favored : 93.35 % Rotamer: Outliers : 2.39 % Allowed : 27.80 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.30), residues: 857 helix: 1.88 (0.26), residues: 424 sheet: 0.55 (0.53), residues: 124 loop : -1.71 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 943 TYR 0.009 0.001 TYR A 842 PHE 0.012 0.001 PHE A 729 TRP 0.006 0.001 TRP A 68 HIS 0.006 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7604) covalent geometry : angle 0.52355 (10522) hydrogen bonds : bond 0.04873 ( 326) hydrogen bonds : angle 4.13867 ( 906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.172 Fit side-chains REVERT: A 438 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: A 511 MET cc_start: 0.9553 (mmt) cc_final: 0.9270 (mmm) REVERT: A 960 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8819 (tm-30) outliers start: 16 outliers final: 5 residues processed: 70 average time/residue: 0.0564 time to fit residues: 6.1687 Evaluate side-chains 63 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 960 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 0.0000 chunk 43 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.059213 restraints weight = 17109.352| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.22 r_work: 0.2700 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7604 Z= 0.109 Angle : 0.491 9.903 10522 Z= 0.258 Chirality : 0.038 0.259 1222 Planarity : 0.003 0.036 1196 Dihedral : 18.835 87.450 1328 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.53 % Favored : 93.00 % Rotamer: Outliers : 3.59 % Allowed : 26.46 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.31), residues: 857 helix: 2.34 (0.26), residues: 428 sheet: 0.61 (0.53), residues: 124 loop : -1.67 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 943 TYR 0.009 0.001 TYR A 842 PHE 0.010 0.001 PHE A 729 TRP 0.008 0.001 TRP A 68 HIS 0.004 0.000 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7604) covalent geometry : angle 0.49093 (10522) hydrogen bonds : bond 0.03521 ( 326) hydrogen bonds : angle 3.62033 ( 906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.232 Fit side-chains REVERT: A 438 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8719 (mp0) REVERT: A 960 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8767 (tm-30) outliers start: 24 outliers final: 9 residues processed: 77 average time/residue: 0.0683 time to fit residues: 7.8925 Evaluate side-chains 64 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 12 optimal weight: 5.9990 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.059926 restraints weight = 17416.299| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.24 r_work: 0.2716 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7604 Z= 0.099 Angle : 0.490 11.535 10522 Z= 0.254 Chirality : 0.038 0.288 1222 Planarity : 0.003 0.037 1196 Dihedral : 18.798 87.120 1328 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.42 % Favored : 93.12 % Rotamer: Outliers : 2.69 % Allowed : 27.06 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.31), residues: 857 helix: 2.46 (0.26), residues: 428 sheet: 0.58 (0.53), residues: 124 loop : -1.64 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 943 TYR 0.008 0.001 TYR A 842 PHE 0.009 0.001 PHE A 729 TRP 0.007 0.001 TRP A 68 HIS 0.003 0.000 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 7604) covalent geometry : angle 0.48983 (10522) hydrogen bonds : bond 0.03053 ( 326) hydrogen bonds : angle 3.43625 ( 906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.278 Fit side-chains REVERT: A 438 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8788 (mp0) REVERT: A 534 ASN cc_start: 0.8395 (m110) cc_final: 0.8185 (m110) outliers start: 18 outliers final: 12 residues processed: 73 average time/residue: 0.0617 time to fit residues: 6.7370 Evaluate side-chains 67 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.057218 restraints weight = 17407.786| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.31 r_work: 0.2590 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7604 Z= 0.147 Angle : 0.492 7.470 10522 Z= 0.261 Chirality : 0.039 0.203 1222 Planarity : 0.003 0.039 1196 Dihedral : 18.844 86.662 1328 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.12 % Favored : 92.53 % Rotamer: Outliers : 3.74 % Allowed : 26.76 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.31), residues: 857 helix: 2.67 (0.26), residues: 424 sheet: 0.58 (0.53), residues: 124 loop : -1.63 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 635 TYR 0.014 0.001 TYR A 842 PHE 0.008 0.001 PHE A 729 TRP 0.007 0.001 TRP A 68 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7604) covalent geometry : angle 0.49230 (10522) hydrogen bonds : bond 0.03732 ( 326) hydrogen bonds : angle 3.55299 ( 906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.227 Fit side-chains REVERT: A 438 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8980 (mp0) REVERT: A 640 GLU cc_start: 0.8849 (pm20) cc_final: 0.8365 (tp30) REVERT: A 880 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8721 (tp40) outliers start: 25 outliers final: 17 residues processed: 74 average time/residue: 0.0614 time to fit residues: 6.9419 Evaluate side-chains 69 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 880 GLN Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 985 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.082538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.057335 restraints weight = 17312.554| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.30 r_work: 0.2595 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7604 Z= 0.134 Angle : 0.500 10.024 10522 Z= 0.259 Chirality : 0.039 0.205 1222 Planarity : 0.003 0.039 1196 Dihedral : 18.874 87.047 1328 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 3.44 % Allowed : 27.06 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.31), residues: 857 helix: 2.72 (0.26), residues: 424 sheet: 0.56 (0.53), residues: 124 loop : -1.60 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 943 TYR 0.012 0.001 TYR A 842 PHE 0.008 0.001 PHE A 729 TRP 0.005 0.001 TRP A 887 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7604) covalent geometry : angle 0.49955 (10522) hydrogen bonds : bond 0.03465 ( 326) hydrogen bonds : angle 3.49189 ( 906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.274 Fit side-chains REVERT: A 438 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8975 (mp0) REVERT: A 960 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8670 (tm-30) outliers start: 23 outliers final: 17 residues processed: 72 average time/residue: 0.0622 time to fit residues: 6.7796 Evaluate side-chains 68 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 985 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.057502 restraints weight = 17228.970| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.41 r_work: 0.2624 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7604 Z= 0.100 Angle : 0.478 9.182 10522 Z= 0.249 Chirality : 0.038 0.230 1222 Planarity : 0.003 0.039 1196 Dihedral : 18.834 87.196 1328 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.88 % Favored : 92.65 % Rotamer: Outliers : 3.14 % Allowed : 27.35 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.31), residues: 857 helix: 2.76 (0.26), residues: 423 sheet: 0.64 (0.53), residues: 124 loop : -1.58 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 943 TYR 0.007 0.001 TYR A 842 PHE 0.007 0.000 PHE A 729 TRP 0.006 0.001 TRP A 68 HIS 0.003 0.000 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7604) covalent geometry : angle 0.47755 (10522) hydrogen bonds : bond 0.02781 ( 326) hydrogen bonds : angle 3.30415 ( 906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.301 Fit side-chains REVERT: A 534 ASN cc_start: 0.8338 (m110) cc_final: 0.8120 (m110) REVERT: A 640 GLU cc_start: 0.8893 (pm20) cc_final: 0.8406 (tp30) REVERT: A 880 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8735 (tp40) outliers start: 21 outliers final: 16 residues processed: 70 average time/residue: 0.0659 time to fit residues: 6.9536 Evaluate side-chains 70 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 880 GLN Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 988 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 42 optimal weight: 0.0970 chunk 71 optimal weight: 0.0000 chunk 8 optimal weight: 6.9990 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.058035 restraints weight = 17266.684| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.42 r_work: 0.2638 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7604 Z= 0.095 Angle : 0.493 9.483 10522 Z= 0.252 Chirality : 0.039 0.388 1222 Planarity : 0.003 0.039 1196 Dihedral : 18.819 87.517 1328 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 2.39 % Allowed : 28.70 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.31), residues: 857 helix: 2.73 (0.26), residues: 423 sheet: 0.67 (0.52), residues: 124 loop : -1.55 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 952 TYR 0.007 0.001 TYR A 842 PHE 0.006 0.000 PHE A 729 TRP 0.005 0.001 TRP A 68 HIS 0.002 0.000 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 7604) covalent geometry : angle 0.49306 (10522) hydrogen bonds : bond 0.02645 ( 326) hydrogen bonds : angle 3.28287 ( 906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.273 Fit side-chains REVERT: A 534 ASN cc_start: 0.8330 (m110) cc_final: 0.8111 (m110) REVERT: A 640 GLU cc_start: 0.8870 (pm20) cc_final: 0.8339 (tp30) outliers start: 16 outliers final: 13 residues processed: 66 average time/residue: 0.0650 time to fit residues: 6.5583 Evaluate side-chains 66 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 985 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.057281 restraints weight = 17158.474| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.40 r_work: 0.2618 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7604 Z= 0.110 Angle : 0.490 8.816 10522 Z= 0.252 Chirality : 0.039 0.282 1222 Planarity : 0.003 0.040 1196 Dihedral : 18.813 88.091 1328 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.00 % Favored : 92.65 % Rotamer: Outliers : 2.54 % Allowed : 28.85 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.31), residues: 857 helix: 2.80 (0.26), residues: 424 sheet: 0.66 (0.53), residues: 124 loop : -1.53 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 952 TYR 0.010 0.001 TYR A 842 PHE 0.006 0.001 PHE A 729 TRP 0.006 0.001 TRP A 68 HIS 0.003 0.000 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7604) covalent geometry : angle 0.48965 (10522) hydrogen bonds : bond 0.02953 ( 326) hydrogen bonds : angle 3.31201 ( 906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.305 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 66 average time/residue: 0.0682 time to fit residues: 6.7729 Evaluate side-chains 66 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 985 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 75 optimal weight: 0.0040 chunk 84 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.059570 restraints weight = 16976.741| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.27 r_work: 0.2642 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7604 Z= 0.099 Angle : 0.485 8.969 10522 Z= 0.249 Chirality : 0.038 0.249 1222 Planarity : 0.003 0.039 1196 Dihedral : 18.803 88.350 1328 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 2.39 % Allowed : 29.15 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.31), residues: 857 helix: 2.80 (0.26), residues: 423 sheet: 0.66 (0.52), residues: 124 loop : -1.53 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 952 TYR 0.008 0.001 TYR A 842 PHE 0.006 0.000 PHE A 729 TRP 0.005 0.000 TRP A 68 HIS 0.003 0.000 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7604) covalent geometry : angle 0.48451 (10522) hydrogen bonds : bond 0.02706 ( 326) hydrogen bonds : angle 3.26970 ( 906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.242 Fit side-chains REVERT: A 534 ASN cc_start: 0.8356 (m110) cc_final: 0.7997 (m110) outliers start: 16 outliers final: 14 residues processed: 66 average time/residue: 0.0722 time to fit residues: 7.2312 Evaluate side-chains 68 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 985 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 0.0370 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.0010 chunk 81 optimal weight: 2.9990 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.058333 restraints weight = 17064.458| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.41 r_work: 0.2645 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7604 Z= 0.096 Angle : 0.485 8.862 10522 Z= 0.249 Chirality : 0.038 0.223 1222 Planarity : 0.003 0.040 1196 Dihedral : 18.773 88.807 1328 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 2.24 % Allowed : 29.30 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.31), residues: 857 helix: 2.83 (0.26), residues: 423 sheet: 0.68 (0.52), residues: 124 loop : -1.52 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 952 TYR 0.006 0.001 TYR A 842 PHE 0.006 0.000 PHE A 729 TRP 0.005 0.000 TRP A 68 HIS 0.002 0.000 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 7604) covalent geometry : angle 0.48482 (10522) hydrogen bonds : bond 0.02535 ( 326) hydrogen bonds : angle 3.21366 ( 906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1609.04 seconds wall clock time: 28 minutes 12.68 seconds (1692.68 seconds total)