Starting phenix.real_space_refine on Thu Jul 2 17:23:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxa_43615/07_2026/8vxa_43615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxa_43615/07_2026/8vxa_43615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vxa_43615/07_2026/8vxa_43615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxa_43615/07_2026/8vxa_43615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vxa_43615/07_2026/8vxa_43615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxa_43615/07_2026/8vxa_43615.map" } resolution = 2.79 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 27 5.16 5 C 5877 2.51 5 N 1685 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9431 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 284 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 8946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 8946 Classifications: {'peptide': 1139} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 45, 'TRANS': 1089} Chain breaks: 1 Time building chain proxies: 2.12, per 1000 atoms: 0.22 Number of scatterers: 9431 At special positions: 0 Unit cell: (89.2, 92.545, 112.615, 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 27 16.00 P 24 15.00 O 1818 8.00 N 1685 7.00 C 5877 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: 1.02 Conformation dependent library (CDL) restraints added in 342.6 milliseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 3 sheets defined 60.2% alpha, 7.5% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 50 through 72 Processing helix chain 'A' and resid 75 through 95 removed outlier: 3.735A pdb=" N ALA A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.842A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Processing helix chain 'A' and resid 225 through 247 removed outlier: 3.883A pdb=" N LEU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 removed outlier: 3.859A pdb=" N HIS A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 285 through 299 Processing helix chain 'A' and resid 311 through 319 removed outlier: 4.220A pdb=" N VAL A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.960A pdb=" N ILE A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 removed outlier: 3.504A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 removed outlier: 4.537A pdb=" N ASP A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.636A pdb=" N ALA A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 553 through 567 Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.811A pdb=" N PHE A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 608 Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.686A pdb=" N GLU A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 632 removed outlier: 3.517A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 665 through 668 Processing helix chain 'A' and resid 691 through 700 Processing helix chain 'A' and resid 720 through 733 Processing helix chain 'A' and resid 742 through 760 removed outlier: 4.069A pdb=" N ARG A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 773 Processing helix chain 'A' and resid 786 through 813 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 821 through 830 Processing helix chain 'A' and resid 833 through 840 Processing helix chain 'A' and resid 844 through 865 removed outlier: 3.821A pdb=" N LYS A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 865 " --> pdb=" O TYR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 878 Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 890 through 907 removed outlier: 4.403A pdb=" N GLN A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 925 removed outlier: 4.064A pdb=" N ILE A 917 " --> pdb=" O ALA A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 949 Processing helix chain 'A' and resid 951 through 955 removed outlier: 3.601A pdb=" N VAL A 955 " --> pdb=" O MET A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 Processing helix chain 'A' and resid 973 through 990 Processing helix chain 'A' and resid 993 through 1002 removed outlier: 3.863A pdb=" N THR A 998 " --> pdb=" O GLY A 994 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A1000 " --> pdb=" O THR A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1015 removed outlier: 3.762A pdb=" N ALA A1011 " --> pdb=" O PHE A1007 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1028 removed outlier: 3.727A pdb=" N GLY A1028 " --> pdb=" O LEU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1043 Processing helix chain 'A' and resid 1048 through 1058 Processing helix chain 'A' and resid 1058 through 1067 removed outlier: 3.767A pdb=" N ILE A1062 " --> pdb=" O SER A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1086 removed outlier: 3.740A pdb=" N LEU A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU A1081 " --> pdb=" O VAL A1077 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A1082 " --> pdb=" O MET A1078 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 381 through 383 removed outlier: 3.657A pdb=" N VAL A 405 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 428 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU A 466 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE A 430 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 325 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER A 467 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A 327 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 531 removed outlier: 4.845A pdb=" N TRP A 525 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 517 " --> pdb=" O TRP A 525 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N SER A 527 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU A 515 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 513 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 500 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL A 713 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN A 502 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TYR A 715 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY A 504 " --> pdb=" O TYR A 715 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE A 717 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL A 506 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 572 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER A 663 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 574 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1097 through 1102 removed outlier: 3.623A pdb=" N TYR A1099 " --> pdb=" O PHE A1163 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LEU A1150 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU A1118 " --> pdb=" O LEU A1150 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A1152 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS A1125 " --> pdb=" O ILE A1138 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A1136 " --> pdb=" O VAL A1127 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.29 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: 2848 1.33 - 1.45: 1445 1.45 - 1.57: 5278 1.57 - 1.69: 46 1.69 - 1.80: 46 Bond restraints: 9663 Sorted by residual: bond pdb=" C3' DT C 5 " pdb=" C2' DT C 5 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG B 6 " pdb=" C2' DG B 6 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DC C 6 " pdb=" C2' DC C 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.01e+00 bond pdb=" C3' DC B 12 " pdb=" C2' DC B 12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.29e+00 bond pdb=" C3' DC C 9 " pdb=" C2' DC C 9 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.40e+00 ... (remaining 9658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 13006 1.94 - 3.88: 197 3.88 - 5.82: 15 5.82 - 7.76: 0 7.76 - 9.70: 1 Bond angle restraints: 13219 Sorted by residual: angle pdb=" O4' DG B 3 " pdb=" C4' DG B 3 " pdb=" C3' DG B 3 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT B 10 " pdb=" C4 DT B 10 " pdb=" O4 DT B 10 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT B 2 " pdb=" C4 DT B 2 " pdb=" O4 DT B 2 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.58e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.28 -2.38 6.00e-01 2.78e+00 1.58e+01 ... (remaining 13214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.73: 5401 25.73 - 51.47: 305 51.47 - 77.20: 46 77.20 - 102.94: 5 102.94 - 128.67: 1 Dihedral angle restraints: 5758 sinusoidal: 2477 harmonic: 3281 Sorted by residual: dihedral pdb=" C4' DC C 6 " pdb=" C3' DC C 6 " pdb=" O3' DC C 6 " pdb=" P DC C 7 " ideal model delta sinusoidal sigma weight residual 220.00 91.33 128.67 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" CA ILE A 662 " pdb=" C ILE A 662 " pdb=" N SER A 663 " pdb=" CA SER A 663 " ideal model delta harmonic sigma weight residual 180.00 -162.70 -17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASN A 672 " pdb=" C ASN A 672 " pdb=" N LEU A 673 " pdb=" CA LEU A 673 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 865 0.027 - 0.054: 402 0.054 - 0.082: 138 0.082 - 0.109: 79 0.109 - 0.136: 17 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA ILE A 817 " pdb=" N ILE A 817 " pdb=" C ILE A 817 " pdb=" CB ILE A 817 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" C3' DC C 6 " pdb=" C4' DC C 6 " pdb=" O3' DC C 6 " pdb=" C2' DC C 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE A 381 " pdb=" N ILE A 381 " pdb=" C ILE A 381 " pdb=" CB ILE A 381 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1498 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " 0.025 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP A 35 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 563 " -0.012 2.00e-02 2.50e+03 1.27e-02 4.06e+00 pdb=" CG TRP A 563 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 563 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 563 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 563 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 563 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 563 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 563 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 563 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 563 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 375 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 376 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.024 5.00e-02 4.00e+02 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 946 2.74 - 3.28: 9537 3.28 - 3.82: 16768 3.82 - 4.36: 19865 4.36 - 4.90: 32995 Nonbonded interactions: 80111 Sorted by model distance: nonbonded pdb=" OE2 GLU A 395 " pdb=" OH TYR A1003 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR A 357 " pdb=" OG SER A 363 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLU A 304 " pdb=" NH2 ARG A 337 " model vdw 2.251 3.120 nonbonded pdb=" NH1 ARG A 454 " pdb=" O ASP A 828 " model vdw 2.272 3.120 nonbonded pdb=" NH2 ARG A 685 " pdb=" OE1 GLU A 694 " model vdw 2.275 3.120 ... (remaining 80106 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.560 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.004 0.041 9663 Z= 0.227 Angle : 0.556 9.703 13219 Z= 0.350 Chirality : 0.040 0.136 1501 Planarity : 0.004 0.043 1638 Dihedral : 15.673 128.673 3638 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.60 (0.25), residues: 1135 helix: 1.12 (0.21), residues: 626 sheet: 0.12 (0.64), residues: 79 loop : -0.54 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 165 TYR 0.013 0.001 TYR A 445 PHE 0.023 0.002 PHE A 413 TRP 0.057 0.002 TRP A 35 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.23 ( 9663) covalent geometry : angle 0.55580 / 0.35 (13219) hydrogen bonds : bond 0.15970 / 17.45 ( 499) hydrogen bonds : angle 5.91833 / 5.74 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 PHE cc_start: 0.8083 (t80) cc_final: 0.7798 (t80) REVERT: A 153 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7158 (mtt180) REVERT: A 264 ASP cc_start: 0.7024 (p0) cc_final: 0.6809 (p0) REVERT: A 322 ASN cc_start: 0.7133 (t0) cc_final: 0.6886 (t0) REVERT: A 382 SER cc_start: 0.7640 (m) cc_final: 0.7419 (t) REVERT: A 383 MET cc_start: 0.7155 (ttt) cc_final: 0.6864 (ttp) REVERT: A 472 ASP cc_start: 0.6824 (m-30) cc_final: 0.6347 (m-30) REVERT: A 548 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7468 (mtmm) REVERT: A 649 ILE cc_start: 0.7968 (tt) cc_final: 0.7610 (pt) REVERT: A 709 VAL cc_start: 0.8683 (p) cc_final: 0.8418 (t) REVERT: A 764 LYS cc_start: 0.6737 (tptt) cc_final: 0.6404 (tptt) REVERT: A 819 ASP cc_start: 0.6905 (t70) cc_final: 0.6683 (t0) REVERT: A 831 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6985 (mm-40) REVERT: A 1169 ASP cc_start: 0.7219 (t0) cc_final: 0.6970 (t70) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.5766 time to fit residues: 147.0700 Evaluate side-chains 194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0010 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 495 ASN A 669 GLN A 686 ASN A 772 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143288 restraints weight = 12373.645| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.66 r_work: 0.3736 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9663 Z= 0.183 Angle : 0.605 10.374 13219 Z= 0.324 Chirality : 0.043 0.243 1501 Planarity : 0.005 0.052 1638 Dihedral : 15.231 131.116 1522 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.32 % Allowed : 10.44 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.52 (0.25), residues: 1135 helix: 1.14 (0.20), residues: 635 sheet: -0.52 (0.63), residues: 76 loop : -0.61 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 758 TYR 0.017 0.002 TYR A 125 PHE 0.022 0.002 PHE A 413 TRP 0.027 0.002 TRP A 35 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 9663) covalent geometry : angle 0.60547 / 0.32 (13219) hydrogen bonds : bond 0.04777 / 5.07 ( 499) hydrogen bonds : angle 4.91110 / 4.98 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.7208 (ttmm) cc_final: 0.6856 (tppt) REVERT: A 264 ASP cc_start: 0.7431 (p0) cc_final: 0.7167 (p0) REVERT: A 322 ASN cc_start: 0.7744 (t0) cc_final: 0.7485 (t0) REVERT: A 328 SER cc_start: 0.8403 (t) cc_final: 0.8112 (p) REVERT: A 400 GLN cc_start: 0.7627 (mp10) cc_final: 0.7375 (mp10) REVERT: A 440 GLU cc_start: 0.7436 (pt0) cc_final: 0.7226 (pt0) REVERT: A 445 TYR cc_start: 0.8401 (t80) cc_final: 0.8065 (t80) REVERT: A 470 LEU cc_start: 0.7988 (mt) cc_final: 0.7725 (mt) REVERT: A 472 ASP cc_start: 0.7302 (m-30) cc_final: 0.7070 (m-30) REVERT: A 493 LYS cc_start: 0.8166 (tppp) cc_final: 0.7850 (tttm) REVERT: A 552 SER cc_start: 0.8509 (t) cc_final: 0.8284 (p) REVERT: A 555 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7796 (ttpt) REVERT: A 649 ILE cc_start: 0.8230 (tt) cc_final: 0.7759 (pt) REVERT: A 671 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 672 ASN cc_start: 0.8036 (t0) cc_final: 0.7756 (t0) REVERT: A 701 ARG cc_start: 0.8224 (mmt180) cc_final: 0.7959 (mmt180) REVERT: A 709 VAL cc_start: 0.8913 (p) cc_final: 0.8648 (t) REVERT: A 715 TYR cc_start: 0.8395 (t80) cc_final: 0.8180 (t80) REVERT: A 740 MET cc_start: 0.8475 (mmm) cc_final: 0.7843 (mmm) REVERT: A 819 ASP cc_start: 0.7558 (t70) cc_final: 0.7296 (t0) REVERT: A 831 GLN cc_start: 0.7729 (tp-100) cc_final: 0.7506 (mm-40) REVERT: A 836 GLN cc_start: 0.8025 (tt0) cc_final: 0.7809 (tt0) REVERT: A 864 GLN cc_start: 0.7893 (tt0) cc_final: 0.7686 (tt0) REVERT: A 1018 SER cc_start: 0.8010 (m) cc_final: 0.7747 (t) REVERT: A 1029 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.5880 (m-80) REVERT: A 1124 ILE cc_start: 0.7999 (tp) cc_final: 0.7695 (pt) REVERT: A 1169 ASP cc_start: 0.7371 (t0) cc_final: 0.7049 (t70) REVERT: A 1170 ASP cc_start: 0.6922 (p0) cc_final: 0.6698 (p0) outliers start: 22 outliers final: 9 residues processed: 218 average time/residue: 0.5770 time to fit residues: 134.0244 Evaluate side-chains 207 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 GLN Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 HIS A 495 ASN A 772 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.158175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141332 restraints weight = 12352.203| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.68 r_work: 0.3718 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9663 Z= 0.203 Angle : 0.594 10.402 13219 Z= 0.318 Chirality : 0.044 0.267 1501 Planarity : 0.005 0.051 1638 Dihedral : 15.305 133.217 1522 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.85 % Allowed : 13.08 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.50 (0.25), residues: 1135 helix: 1.11 (0.20), residues: 639 sheet: -0.64 (0.61), residues: 77 loop : -0.61 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 758 TYR 0.014 0.002 TYR A 125 PHE 0.023 0.002 PHE A 413 TRP 0.022 0.002 TRP A 35 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 9663) covalent geometry : angle 0.59390 / 0.32 (13219) hydrogen bonds : bond 0.04440 / 4.73 ( 499) hydrogen bonds : angle 4.77116 / 4.91 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7246 (t70) cc_final: 0.7027 (t0) REVERT: A 264 ASP cc_start: 0.7453 (p0) cc_final: 0.7164 (p0) REVERT: A 322 ASN cc_start: 0.7757 (t0) cc_final: 0.7474 (t0) REVERT: A 328 SER cc_start: 0.8407 (t) cc_final: 0.8082 (p) REVERT: A 400 GLN cc_start: 0.7693 (mp10) cc_final: 0.7380 (mp10) REVERT: A 401 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.5452 (mpp-170) REVERT: A 445 TYR cc_start: 0.8414 (t80) cc_final: 0.8105 (t80) REVERT: A 548 LYS cc_start: 0.8305 (mtmm) cc_final: 0.8022 (mtmm) REVERT: A 649 ILE cc_start: 0.8253 (tt) cc_final: 0.7769 (pt) REVERT: A 671 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 672 ASN cc_start: 0.7967 (t0) cc_final: 0.7689 (t0) REVERT: A 709 VAL cc_start: 0.8913 (p) cc_final: 0.8640 (t) REVERT: A 740 MET cc_start: 0.8428 (mmm) cc_final: 0.7869 (mmm) REVERT: A 779 PHE cc_start: 0.8428 (t80) cc_final: 0.8139 (t80) REVERT: A 814 GLU cc_start: 0.6899 (tp30) cc_final: 0.6572 (tp30) REVERT: A 819 ASP cc_start: 0.7566 (t70) cc_final: 0.7303 (t0) REVERT: A 831 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7521 (mm-40) REVERT: A 836 GLN cc_start: 0.8063 (tt0) cc_final: 0.7841 (tt0) REVERT: A 864 GLN cc_start: 0.7830 (tt0) cc_final: 0.7619 (tt0) REVERT: A 1018 SER cc_start: 0.8063 (m) cc_final: 0.7823 (t) REVERT: A 1029 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.5650 (m-80) REVERT: A 1169 ASP cc_start: 0.7367 (t0) cc_final: 0.7107 (t70) REVERT: A 1170 ASP cc_start: 0.7015 (p0) cc_final: 0.6768 (p0) outliers start: 27 outliers final: 15 residues processed: 217 average time/residue: 0.5593 time to fit residues: 129.4086 Evaluate side-chains 206 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 0.6980 chunk 106 optimal weight: 0.0970 chunk 93 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN A 815 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142407 restraints weight = 12514.831| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.71 r_work: 0.3735 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9663 Z= 0.137 Angle : 0.545 9.639 13219 Z= 0.292 Chirality : 0.041 0.272 1501 Planarity : 0.005 0.047 1638 Dihedral : 15.270 133.984 1522 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.95 % Allowed : 15.30 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1135 helix: 1.31 (0.20), residues: 639 sheet: -0.55 (0.62), residues: 77 loop : -0.54 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 758 TYR 0.012 0.001 TYR A 445 PHE 0.016 0.001 PHE A 413 TRP 0.016 0.002 TRP A 35 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9663) covalent geometry : angle 0.54514 / 0.29 (13219) hydrogen bonds : bond 0.03794 / 4.02 ( 499) hydrogen bonds : angle 4.60920 / 4.71 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7201 (pp) REVERT: A 151 ASP cc_start: 0.7376 (t0) cc_final: 0.7118 (t0) REVERT: A 210 TYR cc_start: 0.8031 (t80) cc_final: 0.7598 (t80) REVERT: A 235 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6887 (tppt) REVERT: A 264 ASP cc_start: 0.7466 (p0) cc_final: 0.7142 (p0) REVERT: A 322 ASN cc_start: 0.7809 (t0) cc_final: 0.7553 (t0) REVERT: A 400 GLN cc_start: 0.7657 (mp10) cc_final: 0.7362 (mp10) REVERT: A 432 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7115 (mm-30) REVERT: A 445 TYR cc_start: 0.8400 (t80) cc_final: 0.8059 (t80) REVERT: A 649 ILE cc_start: 0.8215 (tt) cc_final: 0.7706 (pt) REVERT: A 672 ASN cc_start: 0.8000 (t0) cc_final: 0.7729 (t0) REVERT: A 709 VAL cc_start: 0.8915 (p) cc_final: 0.8636 (t) REVERT: A 740 MET cc_start: 0.8438 (mmm) cc_final: 0.7869 (mmm) REVERT: A 814 GLU cc_start: 0.6934 (tp30) cc_final: 0.6650 (tp30) REVERT: A 819 ASP cc_start: 0.7543 (t70) cc_final: 0.7277 (t0) REVERT: A 831 GLN cc_start: 0.7797 (tp-100) cc_final: 0.7553 (mm-40) REVERT: A 836 GLN cc_start: 0.8123 (tt0) cc_final: 0.7868 (tt0) REVERT: A 864 GLN cc_start: 0.7876 (tt0) cc_final: 0.7654 (tt0) REVERT: A 897 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7403 (mm) REVERT: A 1018 SER cc_start: 0.7995 (m) cc_final: 0.7727 (t) REVERT: A 1029 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.5787 (m-80) REVERT: A 1099 TYR cc_start: 0.8059 (m-10) cc_final: 0.7846 (m-80) REVERT: A 1170 ASP cc_start: 0.7032 (p0) cc_final: 0.6801 (p0) outliers start: 28 outliers final: 19 residues processed: 209 average time/residue: 0.5200 time to fit residues: 116.1397 Evaluate side-chains 219 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 98 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 52 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 495 ASN A 815 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.158998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141695 restraints weight = 12434.585| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.71 r_work: 0.3726 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9663 Z= 0.158 Angle : 0.547 9.878 13219 Z= 0.292 Chirality : 0.042 0.271 1501 Planarity : 0.005 0.043 1638 Dihedral : 15.261 134.450 1522 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.06 % Allowed : 17.30 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.73 (0.25), residues: 1135 helix: 1.34 (0.20), residues: 640 sheet: -0.52 (0.61), residues: 77 loop : -0.57 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 758 TYR 0.011 0.002 TYR A 445 PHE 0.010 0.001 PHE A 779 TRP 0.016 0.002 TRP A 35 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 9663) covalent geometry : angle 0.54740 / 0.29 (13219) hydrogen bonds : bond 0.03840 / 4.06 ( 499) hydrogen bonds : angle 4.55577 / 4.65 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7186 (pp) REVERT: A 151 ASP cc_start: 0.7415 (t0) cc_final: 0.7118 (t0) REVERT: A 264 ASP cc_start: 0.7486 (p0) cc_final: 0.7134 (p0) REVERT: A 312 ARG cc_start: 0.7999 (mpp80) cc_final: 0.7767 (mtm-85) REVERT: A 322 ASN cc_start: 0.7768 (t0) cc_final: 0.7497 (t0) REVERT: A 432 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 445 TYR cc_start: 0.8409 (t80) cc_final: 0.8100 (t80) REVERT: A 548 LYS cc_start: 0.8291 (mtmm) cc_final: 0.7943 (mtmm) REVERT: A 649 ILE cc_start: 0.8212 (tt) cc_final: 0.7962 (mp) REVERT: A 709 VAL cc_start: 0.8980 (p) cc_final: 0.8691 (t) REVERT: A 740 MET cc_start: 0.8424 (mmm) cc_final: 0.7913 (mmm) REVERT: A 779 PHE cc_start: 0.8298 (t80) cc_final: 0.7913 (t80) REVERT: A 814 GLU cc_start: 0.6924 (tp30) cc_final: 0.6623 (tp30) REVERT: A 819 ASP cc_start: 0.7536 (t70) cc_final: 0.7273 (t0) REVERT: A 831 GLN cc_start: 0.7814 (tp-100) cc_final: 0.7548 (mm-40) REVERT: A 836 GLN cc_start: 0.8070 (tt0) cc_final: 0.7805 (tt0) REVERT: A 864 GLN cc_start: 0.7878 (tt0) cc_final: 0.7662 (tt0) REVERT: A 897 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7421 (mm) REVERT: A 1018 SER cc_start: 0.8046 (m) cc_final: 0.7777 (t) REVERT: A 1029 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.5804 (m-80) REVERT: A 1099 TYR cc_start: 0.8012 (m-10) cc_final: 0.7794 (m-10) REVERT: A 1162 MET cc_start: 0.7230 (tmm) cc_final: 0.6918 (tpt) REVERT: A 1170 ASP cc_start: 0.7069 (p0) cc_final: 0.6847 (p0) outliers start: 29 outliers final: 18 residues processed: 216 average time/residue: 0.5545 time to fit residues: 127.7569 Evaluate side-chains 221 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 15 optimal weight: 0.0870 chunk 43 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 400 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.141899 restraints weight = 12452.871| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.66 r_work: 0.3734 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9663 Z= 0.175 Angle : 0.555 9.852 13219 Z= 0.297 Chirality : 0.042 0.269 1501 Planarity : 0.005 0.047 1638 Dihedral : 15.278 134.576 1522 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.27 % Allowed : 17.83 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1135 helix: 1.32 (0.20), residues: 639 sheet: -0.52 (0.61), residues: 76 loop : -0.55 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 758 TYR 0.012 0.002 TYR A 217 PHE 0.011 0.001 PHE A1029 TRP 0.016 0.002 TRP A 35 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 9663) covalent geometry : angle 0.55540 / 0.30 (13219) hydrogen bonds : bond 0.03842 / 4.08 ( 499) hydrogen bonds : angle 4.51733 / 4.62 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.309 Fit side-chains REVERT: A 94 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7249 (pp) REVERT: A 151 ASP cc_start: 0.7424 (t0) cc_final: 0.7200 (t0) REVERT: A 264 ASP cc_start: 0.7480 (p0) cc_final: 0.7173 (p0) REVERT: A 322 ASN cc_start: 0.7583 (t0) cc_final: 0.7351 (t0) REVERT: A 432 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 548 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7945 (mtmm) REVERT: A 552 SER cc_start: 0.8501 (t) cc_final: 0.8285 (p) REVERT: A 649 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 695 PHE cc_start: 0.8224 (t80) cc_final: 0.7845 (t80) REVERT: A 709 VAL cc_start: 0.8966 (p) cc_final: 0.8679 (t) REVERT: A 740 MET cc_start: 0.8420 (mmm) cc_final: 0.7914 (mmm) REVERT: A 779 PHE cc_start: 0.8342 (t80) cc_final: 0.7986 (t80) REVERT: A 814 GLU cc_start: 0.6852 (tp30) cc_final: 0.6625 (tp30) REVERT: A 819 ASP cc_start: 0.7542 (t70) cc_final: 0.7279 (t0) REVERT: A 831 GLN cc_start: 0.7845 (tp-100) cc_final: 0.7588 (mm-40) REVERT: A 836 GLN cc_start: 0.8090 (tt0) cc_final: 0.7831 (tt0) REVERT: A 864 GLN cc_start: 0.7884 (tt0) cc_final: 0.7675 (tt0) REVERT: A 989 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7681 (t0) REVERT: A 1018 SER cc_start: 0.8005 (m) cc_final: 0.7783 (t) REVERT: A 1029 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.5585 (m-80) REVERT: A 1170 ASP cc_start: 0.7084 (p0) cc_final: 0.6874 (p0) outliers start: 31 outliers final: 18 residues processed: 219 average time/residue: 0.5661 time to fit residues: 132.4629 Evaluate side-chains 217 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 400 GLN A1125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.158300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141378 restraints weight = 12445.436| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.67 r_work: 0.3723 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9663 Z= 0.191 Angle : 0.581 9.678 13219 Z= 0.309 Chirality : 0.043 0.266 1501 Planarity : 0.005 0.056 1638 Dihedral : 15.297 134.736 1522 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.27 % Allowed : 18.46 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.63 (0.25), residues: 1135 helix: 1.22 (0.20), residues: 642 sheet: -0.61 (0.59), residues: 76 loop : -0.57 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 758 TYR 0.012 0.002 TYR A 217 PHE 0.031 0.002 PHE A 966 TRP 0.019 0.002 TRP A 525 HIS 0.007 0.001 HIS A1125 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 9663) covalent geometry : angle 0.58088 / 0.31 (13219) hydrogen bonds : bond 0.03947 / 4.22 ( 499) hydrogen bonds : angle 4.56501 / 4.65 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.226 Fit side-chains REVERT: A 94 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7279 (pp) REVERT: A 151 ASP cc_start: 0.7438 (t0) cc_final: 0.7200 (t0) REVERT: A 264 ASP cc_start: 0.7457 (p0) cc_final: 0.7181 (p0) REVERT: A 322 ASN cc_start: 0.7575 (t0) cc_final: 0.7354 (t0) REVERT: A 432 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 548 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7984 (mtmm) REVERT: A 552 SER cc_start: 0.8515 (t) cc_final: 0.8313 (p) REVERT: A 649 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8032 (mp) REVERT: A 695 PHE cc_start: 0.8210 (t80) cc_final: 0.7894 (t80) REVERT: A 709 VAL cc_start: 0.8997 (p) cc_final: 0.8720 (t) REVERT: A 740 MET cc_start: 0.8433 (mmm) cc_final: 0.7942 (mmm) REVERT: A 779 PHE cc_start: 0.8370 (t80) cc_final: 0.7990 (t80) REVERT: A 802 SER cc_start: 0.8228 (t) cc_final: 0.7854 (p) REVERT: A 814 GLU cc_start: 0.6890 (tp30) cc_final: 0.6646 (tp30) REVERT: A 819 ASP cc_start: 0.7567 (t70) cc_final: 0.7308 (t0) REVERT: A 831 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7581 (mm-40) REVERT: A 836 GLN cc_start: 0.8099 (tt0) cc_final: 0.7834 (tt0) REVERT: A 864 GLN cc_start: 0.7899 (tt0) cc_final: 0.7696 (tt0) REVERT: A 989 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7664 (t0) REVERT: A 1018 SER cc_start: 0.7976 (m) cc_final: 0.7752 (t) REVERT: A 1029 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.5561 (m-80) REVERT: A 1099 TYR cc_start: 0.7973 (m-10) cc_final: 0.7604 (m-80) REVERT: A 1102 MET cc_start: 0.6218 (tpp) cc_final: 0.5656 (mpp) REVERT: A 1124 ILE cc_start: 0.7897 (tp) cc_final: 0.7677 (pt) REVERT: A 1160 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6480 (mtm-85) REVERT: A 1162 MET cc_start: 0.7282 (tmm) cc_final: 0.6895 (tpt) REVERT: A 1170 ASP cc_start: 0.7081 (p0) cc_final: 0.6878 (p0) outliers start: 31 outliers final: 19 residues processed: 217 average time/residue: 0.5826 time to fit residues: 135.0257 Evaluate side-chains 224 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 100 optimal weight: 0.6980 chunk 112 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 400 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.159004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142039 restraints weight = 12460.465| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.68 r_work: 0.3733 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9663 Z= 0.152 Angle : 0.556 9.519 13219 Z= 0.296 Chirality : 0.041 0.261 1501 Planarity : 0.005 0.057 1638 Dihedral : 15.261 134.577 1522 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.27 % Allowed : 18.99 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.78 (0.25), residues: 1135 helix: 1.35 (0.20), residues: 640 sheet: -0.56 (0.61), residues: 74 loop : -0.48 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 758 TYR 0.011 0.002 TYR A 217 PHE 0.019 0.001 PHE A 966 TRP 0.016 0.002 TRP A 35 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9663) covalent geometry : angle 0.55557 / 0.30 (13219) hydrogen bonds : bond 0.03705 / 3.95 ( 499) hydrogen bonds : angle 4.49464 / 4.60 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.357 Fit side-chains REVERT: A 94 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7231 (pp) REVERT: A 151 ASP cc_start: 0.7430 (t0) cc_final: 0.7188 (t0) REVERT: A 264 ASP cc_start: 0.7403 (p0) cc_final: 0.7155 (p0) REVERT: A 322 ASN cc_start: 0.7591 (t0) cc_final: 0.7374 (t0) REVERT: A 432 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7100 (mm-30) REVERT: A 548 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7951 (mtmm) REVERT: A 552 SER cc_start: 0.8510 (t) cc_final: 0.8296 (p) REVERT: A 649 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8028 (mp) REVERT: A 695 PHE cc_start: 0.8147 (t80) cc_final: 0.7846 (t80) REVERT: A 740 MET cc_start: 0.8432 (mmm) cc_final: 0.7909 (mmm) REVERT: A 802 SER cc_start: 0.8226 (t) cc_final: 0.7853 (p) REVERT: A 819 ASP cc_start: 0.7560 (t70) cc_final: 0.7297 (t0) REVERT: A 831 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7590 (mm-40) REVERT: A 864 GLN cc_start: 0.7911 (tt0) cc_final: 0.7705 (tt0) REVERT: A 897 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7461 (mm) REVERT: A 989 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7636 (t0) REVERT: A 1018 SER cc_start: 0.7967 (m) cc_final: 0.7735 (t) REVERT: A 1029 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.5717 (m-80) REVERT: A 1099 TYR cc_start: 0.7981 (m-10) cc_final: 0.7750 (m-10) REVERT: A 1102 MET cc_start: 0.6155 (tpp) cc_final: 0.5651 (mpp) REVERT: A 1162 MET cc_start: 0.7289 (tmm) cc_final: 0.6930 (tpt) outliers start: 31 outliers final: 20 residues processed: 222 average time/residue: 0.6108 time to fit residues: 144.8407 Evaluate side-chains 225 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 400 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.158333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141464 restraints weight = 12407.231| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.67 r_work: 0.3726 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9663 Z= 0.179 Angle : 0.586 9.735 13219 Z= 0.311 Chirality : 0.043 0.256 1501 Planarity : 0.005 0.062 1638 Dihedral : 15.263 134.871 1522 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.16 % Allowed : 19.73 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.73 (0.25), residues: 1135 helix: 1.28 (0.20), residues: 642 sheet: -0.64 (0.54), residues: 95 loop : -0.42 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 758 TYR 0.011 0.002 TYR A 217 PHE 0.021 0.002 PHE A 966 TRP 0.024 0.002 TRP A 266 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 9663) covalent geometry : angle 0.58626 / 0.31 (13219) hydrogen bonds : bond 0.03844 / 4.11 ( 499) hydrogen bonds : angle 4.51997 / 4.63 ( 1452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.395 Fit side-chains REVERT: A 94 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7224 (pp) REVERT: A 151 ASP cc_start: 0.7478 (t0) cc_final: 0.7203 (t0) REVERT: A 210 TYR cc_start: 0.7812 (t80) cc_final: 0.7595 (t80) REVERT: A 264 ASP cc_start: 0.7393 (p0) cc_final: 0.7132 (p0) REVERT: A 266 TRP cc_start: 0.7230 (t-100) cc_final: 0.6748 (t-100) REVERT: A 322 ASN cc_start: 0.7633 (t0) cc_final: 0.7412 (t0) REVERT: A 432 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7099 (mm-30) REVERT: A 548 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7977 (mtmm) REVERT: A 552 SER cc_start: 0.8528 (t) cc_final: 0.8315 (p) REVERT: A 649 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7962 (mp) REVERT: A 695 PHE cc_start: 0.8107 (t80) cc_final: 0.7786 (t80) REVERT: A 740 MET cc_start: 0.8433 (mmm) cc_final: 0.7909 (mmm) REVERT: A 802 SER cc_start: 0.8224 (t) cc_final: 0.7836 (p) REVERT: A 819 ASP cc_start: 0.7600 (t70) cc_final: 0.7339 (t0) REVERT: A 831 GLN cc_start: 0.7833 (tp-100) cc_final: 0.7627 (mm-40) REVERT: A 989 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7700 (t0) REVERT: A 1018 SER cc_start: 0.8002 (m) cc_final: 0.7733 (t) REVERT: A 1029 PHE cc_start: 0.6656 (OUTLIER) cc_final: 0.5539 (m-80) REVERT: A 1102 MET cc_start: 0.6099 (tpp) cc_final: 0.5610 (mpp) REVERT: A 1162 MET cc_start: 0.7324 (tmm) cc_final: 0.6944 (tpt) outliers start: 30 outliers final: 20 residues processed: 213 average time/residue: 0.6242 time to fit residues: 141.8333 Evaluate side-chains 224 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN A1125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.157971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.141179 restraints weight = 12446.899| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.67 r_work: 0.3727 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9663 Z= 0.188 Angle : 0.593 9.686 13219 Z= 0.316 Chirality : 0.043 0.252 1501 Planarity : 0.005 0.062 1638 Dihedral : 15.260 135.106 1522 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.06 % Allowed : 19.94 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 (0.25), residues: 1135 helix: 1.25 (0.20), residues: 642 sheet: -1.04 (0.56), residues: 84 loop : -0.39 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 758 TYR 0.012 0.002 TYR A 217 PHE 0.020 0.002 PHE A 966 TRP 0.020 0.002 TRP A 266 HIS 0.007 0.001 HIS A1125 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 9663) covalent geometry : angle 0.59308 / 0.32 (13219) hydrogen bonds : bond 0.03866 / 4.13 ( 499) hydrogen bonds : angle 4.52752 / 4.64 ( 1452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.244 Fit side-chains REVERT: A 94 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7253 (pp) REVERT: A 151 ASP cc_start: 0.7455 (t0) cc_final: 0.7189 (t0) REVERT: A 264 ASP cc_start: 0.7362 (p0) cc_final: 0.7138 (p0) REVERT: A 266 TRP cc_start: 0.7162 (t-100) cc_final: 0.6618 (t-100) REVERT: A 432 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 445 TYR cc_start: 0.8469 (t80) cc_final: 0.8164 (t80) REVERT: A 548 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7985 (mtmm) REVERT: A 552 SER cc_start: 0.8529 (t) cc_final: 0.8321 (p) REVERT: A 649 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8021 (mp) REVERT: A 695 PHE cc_start: 0.8123 (t80) cc_final: 0.7815 (t80) REVERT: A 740 MET cc_start: 0.8428 (mmm) cc_final: 0.7904 (mmm) REVERT: A 779 PHE cc_start: 0.8219 (t80) cc_final: 0.7952 (t80) REVERT: A 802 SER cc_start: 0.8256 (t) cc_final: 0.7889 (p) REVERT: A 989 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7692 (t0) REVERT: A 1018 SER cc_start: 0.7995 (m) cc_final: 0.7762 (t) REVERT: A 1029 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.5507 (m-80) REVERT: A 1099 TYR cc_start: 0.8008 (m-10) cc_final: 0.7644 (m-80) REVERT: A 1162 MET cc_start: 0.7353 (tmm) cc_final: 0.7013 (tpt) outliers start: 29 outliers final: 21 residues processed: 214 average time/residue: 0.6234 time to fit residues: 142.4071 Evaluate side-chains 228 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 104 optimal weight: 0.6980 chunk 106 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 400 GLN A 836 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.158931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142095 restraints weight = 12343.125| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.67 r_work: 0.3734 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9663 Z= 0.148 Angle : 0.585 9.656 13219 Z= 0.311 Chirality : 0.043 0.247 1501 Planarity : 0.005 0.061 1638 Dihedral : 15.221 135.096 1522 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.43 % Allowed : 21.62 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.82 (0.25), residues: 1135 helix: 1.34 (0.20), residues: 642 sheet: -0.70 (0.54), residues: 94 loop : -0.34 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 758 TYR 0.013 0.002 TYR A 874 PHE 0.018 0.001 PHE A 966 TRP 0.017 0.002 TRP A 35 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 9663) covalent geometry : angle 0.58485 / 0.31 (13219) hydrogen bonds : bond 0.03638 / 3.89 ( 499) hydrogen bonds : angle 4.46958 / 4.59 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3470.34 seconds wall clock time: 59 minutes 50.70 seconds (3590.70 seconds total)