Starting phenix.real_space_refine on Sun Sep 13 06:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ron_54125/09_2026/9ron_54125_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ron_54125/09_2026/9ron_54125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ron_54125/09_2026/9ron_54125_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ron_54125/09_2026/9ron_54125_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ron_54125/09_2026/9ron_54125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ron_54125/09_2026/9ron_54125.map" } resolution = 3.41 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= 0.013 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 58 5.16 5 C 6564 2.51 5 N 1717 2.21 5 O 1930 1.98 5 H 10280 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 15476 Classifications: {'peptide': 994} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 950} Chain: "B" Number of atoms: 4502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4502 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 257} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.11, per 1000 atoms: 0.15 Number of scatterers: 20552 At special positions: 0 Unit cell: (73.781, 92.019, 169.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 3 15.00 O 1930 8.00 N 1717 7.00 C 6564 6.00 H 10280 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 637.1 milliseconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 50.2% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 99 through 122 removed outlier: 3.631A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 164 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.545A pdb=" N ARG A 264 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 265 " --> pdb=" O GLY A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 332 Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 363 through 369 removed outlier: 4.067A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.916A pdb=" N MET A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 531 through 548 removed outlier: 3.604A pdb=" N LEU A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.619A pdb=" N ALA A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 667 through 673 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 708 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 754 through 782 removed outlier: 3.943A pdb=" N ILE A 758 " --> pdb=" O ASN A 754 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 796 Processing helix chain 'A' and resid 803 through 814 Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.736A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 4.161A pdb=" N ARG A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 856 through 877 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.115A pdb=" N LEU A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 938 removed outlier: 3.927A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 Processing helix chain 'A' and resid 973 through 978 removed outlier: 3.505A pdb=" N ALA A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 990 removed outlier: 3.839A pdb=" N TRP A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.556A pdb=" N SER A 995 " --> pdb=" O ALA A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1021 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.645A pdb=" N VAL B 208 " --> pdb=" O ASN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.532A pdb=" N SER B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.467A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 197 " --> pdb=" O CYS A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.467A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS A 249 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS A 212 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLU A 251 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY A 210 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA4, first strand: chain 'A' and resid 663 through 666 removed outlier: 3.505A pdb=" N VAL A 689 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 730 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 396 through 399 removed outlier: 5.446A pdb=" N VAL A 388 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE A 592 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS A 390 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG A 551 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 508 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN A 489 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 490 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 479 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 492 " --> pdb=" O ILE A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 396 through 399 removed outlier: 5.446A pdb=" N VAL A 388 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE A 592 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS A 390 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 520 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLY A 587 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N LEU A 522 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 11.900A pdb=" N ILE A 589 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 89 removed outlier: 5.540A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 removed outlier: 5.611A pdb=" N VAL B 148 " --> pdb=" O GLU B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 209 through 210 534 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10256 1.03 - 1.23: 34 1.23 - 1.42: 4283 1.42 - 1.62: 6107 1.62 - 1.82: 86 Bond restraints: 20766 Sorted by residual: bond pdb=" C VAL B 72 " pdb=" O VAL B 72 " ideal model delta sigma weight residual 1.236 1.224 0.012 1.19e-02 7.06e+03 1.08e+00 bond pdb=" CB LYS B 96 " pdb=" CG LYS B 96 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.29e-01 bond pdb=" CB ASN A 360 " pdb=" CG ASN A 360 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.84e-01 bond pdb=" CB LYS B 221 " pdb=" CG LYS B 221 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.95e-01 bond pdb=" CA VAL A 586 " pdb=" CB VAL A 586 " ideal model delta sigma weight residual 1.545 1.538 0.007 9.10e-03 1.21e+04 6.23e-01 ... (remaining 20761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 37292 1.92 - 3.84: 314 3.84 - 5.77: 23 5.77 - 7.69: 7 7.69 - 9.61: 2 Bond angle restraints: 37638 Sorted by residual: angle pdb=" CB MET A 852 " pdb=" CG MET A 852 " pdb=" SD MET A 852 " ideal model delta sigma weight residual 112.70 122.31 -9.61 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CB MET B 268 " pdb=" CG MET B 268 " pdb=" SD MET B 268 " ideal model delta sigma weight residual 112.70 122.20 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" CA LYS B 96 " pdb=" CB LYS B 96 " pdb=" CG LYS B 96 " ideal model delta sigma weight residual 114.10 119.98 -5.88 2.00e+00 2.50e-01 8.64e+00 angle pdb=" CB MET B 121 " pdb=" CG MET B 121 " pdb=" SD MET B 121 " ideal model delta sigma weight residual 112.70 120.13 -7.43 3.00e+00 1.11e-01 6.13e+00 angle pdb=" N ASN A 360 " pdb=" CA ASN A 360 " pdb=" C ASN A 360 " ideal model delta sigma weight residual 110.91 108.18 2.73 1.17e+00 7.31e-01 5.46e+00 ... (remaining 37633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8517 17.82 - 35.64: 877 35.64 - 53.46: 288 53.46 - 71.28: 81 71.28 - 89.10: 13 Dihedral angle restraints: 9776 sinusoidal: 5392 harmonic: 4384 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 170.40 -77.40 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CA MET A 164 " pdb=" C MET A 164 " pdb=" N VAL A 165 " pdb=" CA VAL A 165 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PRO A 839 " pdb=" C PRO A 839 " pdb=" N LYS A 840 " pdb=" CA LYS A 840 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 9773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1388 0.058 - 0.115: 204 0.115 - 0.173: 13 0.173 - 0.230: 0 0.230 - 0.288: 3 Chirality restraints: 1608 Sorted by residual: chirality pdb=" C2' ATP A1101 " pdb=" C1' ATP A1101 " pdb=" C3' ATP A1101 " pdb=" O2' ATP A1101 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C3' ATP A1101 " pdb=" C2' ATP A1101 " pdb=" C4' ATP A1101 " pdb=" O3' ATP A1101 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C4' ATP A1101 " pdb=" C3' ATP A1101 " pdb=" C5' ATP A1101 " pdb=" O4' ATP A1101 " both_signs ideal model delta sigma weight residual False -2.49 -2.75 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1605 not shown) Planarity restraints: 3070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 784 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO A 785 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 785 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 785 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 360 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ASN A 360 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN A 360 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 361 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 620 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 621 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.020 5.00e-02 4.00e+02 ... (remaining 3067 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 949 2.14 - 2.75: 40059 2.75 - 3.37: 62555 3.37 - 3.98: 77547 3.98 - 4.60: 119377 Nonbonded interactions: 300487 Sorted by model distance: nonbonded pdb=" H GLY A 196 " pdb=" O CYS A 249 " model vdw 1.523 2.450 nonbonded pdb=" H GLY A 735 " pdb=" OD1 ASP A 753 " model vdw 1.535 2.450 nonbonded pdb=" OE1 GLU B 87 " pdb=" H GLU B 87 " model vdw 1.579 2.450 nonbonded pdb=" OD1 ASP A 128 " pdb=" H ASN A 129 " model vdw 1.579 2.450 nonbonded pdb=" HG1 THR A 781 " pdb=" OD2 ASP A 933 " model vdw 1.580 2.450 ... (remaining 300482 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=0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.080 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: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.870 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10489 Z= 0.124 Angle : 0.584 9.611 14228 Z= 0.292 Chirality : 0.041 0.288 1608 Planarity : 0.003 0.062 1831 Dihedral : 15.888 89.105 3917 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 0.36 % Allowed : 18.63 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.01 (0.24), residues: 1300 helix: 1.13 (0.22), residues: 577 sheet: -0.76 (0.50), residues: 109 loop : -0.92 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 27 TYR 0.009 0.001 TYR A 994 PHE 0.012 0.001 PHE A 161 TRP 0.020 0.001 TRP A 418 HIS 0.003 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10486) covalent geometry : angle 0.58419 / 0.29 (14222) SS BOND : bond 0.00076 / 0.04 ( 3) SS BOND : angle 0.88287 / 0.43 ( 6) hydrogen bonds : bond 0.17624 / 12.37 ( 514) hydrogen bonds : angle 7.07824 / 5.05 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 115 average time/residue: 0.1617 time to fit residues: 29.1873 Evaluate side-chains 111 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain B residue 218 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.106330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068925 restraints weight = 88330.978| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 4.51 r_work: 0.2975 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10489 Z= 0.149 Angle : 0.581 6.461 14228 Z= 0.305 Chirality : 0.041 0.163 1608 Planarity : 0.004 0.060 1831 Dihedral : 7.030 85.348 1448 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.62 % Favored : 94.23 % Rotamer: Outliers : 1.43 % Allowed : 16.84 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.24 (0.24), residues: 1300 helix: 1.44 (0.21), residues: 581 sheet: -0.61 (0.50), residues: 109 loop : -0.96 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.010 0.001 TYR A 994 PHE 0.010 0.001 PHE A 793 TRP 0.010 0.001 TRP A 418 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (10486) covalent geometry : angle 0.58046 / 0.31 (14222) SS BOND : bond 0.00160 / 0.08 ( 3) SS BOND : angle 0.93936 / 0.51 ( 6) hydrogen bonds : bond 0.04856 / 3.32 ( 514) hydrogen bonds : angle 5.44977 / 3.81 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 TYR cc_start: 0.9061 (t80) cc_final: 0.8853 (t80) REVERT: B 268 MET cc_start: 0.9042 (tpp) cc_final: 0.8830 (tpp) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.1808 time to fit residues: 34.9855 Evaluate side-chains 120 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain C residue 53 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 46 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.104885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067982 restraints weight = 88987.456| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 4.32 r_work: 0.2952 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10489 Z= 0.260 Angle : 0.598 5.986 14228 Z= 0.324 Chirality : 0.041 0.151 1608 Planarity : 0.004 0.061 1831 Dihedral : 7.135 86.323 1447 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.77 % Favored : 93.08 % Rotamer: Outliers : 2.41 % Allowed : 17.02 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.03 (0.23), residues: 1300 helix: 1.28 (0.21), residues: 580 sheet: -0.77 (0.49), residues: 109 loop : -1.16 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 979 TYR 0.015 0.001 TYR A 869 PHE 0.011 0.001 PHE A 245 TRP 0.011 0.001 TRP A 418 HIS 0.004 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.26 (10486) covalent geometry : angle 0.59769 / 0.32 (14222) SS BOND : bond 0.00051 / 0.03 ( 3) SS BOND : angle 1.02949 / 0.54 ( 6) hydrogen bonds : bond 0.04603 / 3.18 ( 514) hydrogen bonds : angle 5.33417 / 3.71 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8961 (mmmt) REVERT: B 87 GLU cc_start: 0.8946 (pm20) cc_final: 0.8725 (pm20) outliers start: 27 outliers final: 17 residues processed: 126 average time/residue: 0.1778 time to fit residues: 35.4207 Evaluate side-chains 120 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain C residue 53 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 60 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.105208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067654 restraints weight = 89277.059| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.46 r_work: 0.2944 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10489 Z= 0.177 Angle : 0.569 6.328 14228 Z= 0.300 Chirality : 0.040 0.144 1608 Planarity : 0.004 0.061 1831 Dihedral : 7.052 85.629 1447 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.92 % Favored : 93.92 % Rotamer: Outliers : 2.50 % Allowed : 18.00 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.02 (0.23), residues: 1300 helix: 1.35 (0.21), residues: 576 sheet: -0.95 (0.49), residues: 111 loop : -1.10 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 445 TYR 0.012 0.001 TYR A 994 PHE 0.009 0.001 PHE B 108 TRP 0.011 0.001 TRP A 418 HIS 0.003 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (10486) covalent geometry : angle 0.56886 / 0.30 (14222) SS BOND : bond 0.00121 / 0.06 ( 3) SS BOND : angle 1.01620 / 0.54 ( 6) hydrogen bonds : bond 0.04192 / 2.88 ( 514) hydrogen bonds : angle 5.12597 / 3.57 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 21 residues processed: 135 average time/residue: 0.1810 time to fit residues: 39.1652 Evaluate side-chains 127 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 53 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 34 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 40.0000 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.104337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.067384 restraints weight = 88959.377| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.36 r_work: 0.2924 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10489 Z= 0.234 Angle : 0.589 6.420 14228 Z= 0.315 Chirality : 0.040 0.152 1608 Planarity : 0.004 0.062 1831 Dihedral : 7.109 87.553 1447 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.23 % Favored : 92.62 % Rotamer: Outliers : 2.94 % Allowed : 17.91 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.11 (0.23), residues: 1300 helix: 1.24 (0.21), residues: 582 sheet: -1.17 (0.47), residues: 117 loop : -1.15 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 837 TYR 0.013 0.001 TYR A 869 PHE 0.013 0.001 PHE A 393 TRP 0.013 0.001 TRP A 894 HIS 0.008 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (10486) covalent geometry : angle 0.58637 / 0.31 (14222) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 2.73059 / 1.56 ( 6) hydrogen bonds : bond 0.04159 / 2.87 ( 514) hydrogen bonds : angle 5.11986 / 3.56 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: A 267 MET cc_start: 0.8845 (mmm) cc_final: 0.8609 (mmm) REVERT: A 588 LEU cc_start: 0.9515 (mp) cc_final: 0.9279 (mm) REVERT: B 87 GLU cc_start: 0.8952 (pm20) cc_final: 0.8734 (pm20) outliers start: 33 outliers final: 31 residues processed: 131 average time/residue: 0.1838 time to fit residues: 38.2740 Evaluate side-chains 133 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 53 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 50 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.104409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067624 restraints weight = 87723.207| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.27 r_work: 0.2928 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10489 Z= 0.228 Angle : 0.588 6.830 14228 Z= 0.314 Chirality : 0.041 0.150 1608 Planarity : 0.004 0.062 1831 Dihedral : 7.083 88.588 1447 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.15 % Rotamer: Outliers : 3.21 % Allowed : 18.45 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.19 (0.23), residues: 1300 helix: 1.16 (0.21), residues: 579 sheet: -1.28 (0.46), residues: 122 loop : -1.16 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 837 TYR 0.013 0.001 TYR A 994 PHE 0.010 0.001 PHE A 245 TRP 0.011 0.001 TRP A 418 HIS 0.008 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.23 (10486) covalent geometry : angle 0.58736 / 0.31 (14222) SS BOND : bond 0.00192 / 0.10 ( 3) SS BOND : angle 1.85119 / 1.01 ( 6) hydrogen bonds : bond 0.04107 / 2.83 ( 514) hydrogen bonds : angle 5.06716 / 3.52 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7971 (pt0) REVERT: A 588 LEU cc_start: 0.9517 (mp) cc_final: 0.9281 (mm) REVERT: B 275 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8041 (mp0) outliers start: 36 outliers final: 32 residues processed: 134 average time/residue: 0.1767 time to fit residues: 37.6378 Evaluate side-chains 134 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 53 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 3 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.105697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069103 restraints weight = 86163.642| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 4.30 r_work: 0.2960 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10489 Z= 0.121 Angle : 0.564 7.164 14228 Z= 0.290 Chirality : 0.040 0.137 1608 Planarity : 0.004 0.061 1831 Dihedral : 6.894 87.139 1447 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer: Outliers : 2.67 % Allowed : 19.25 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.05 (0.24), residues: 1300 helix: 1.37 (0.21), residues: 586 sheet: -1.23 (0.46), residues: 121 loop : -1.05 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 607 TYR 0.011 0.001 TYR A 994 PHE 0.011 0.001 PHE A 244 TRP 0.014 0.001 TRP A 418 HIS 0.005 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10486) covalent geometry : angle 0.56329 / 0.29 (14222) SS BOND : bond 0.00157 / 0.08 ( 3) SS BOND : angle 1.26586 / 0.70 ( 6) hydrogen bonds : bond 0.03862 / 2.66 ( 514) hydrogen bonds : angle 4.79428 / 3.33 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8170 (tp) REVERT: A 588 LEU cc_start: 0.9520 (mp) cc_final: 0.9313 (mm) REVERT: B 87 GLU cc_start: 0.8908 (pm20) cc_final: 0.8696 (pm20) REVERT: B 275 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7964 (mp0) outliers start: 30 outliers final: 24 residues processed: 140 average time/residue: 0.1774 time to fit residues: 39.5477 Evaluate side-chains 132 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 38 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.106211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069344 restraints weight = 87482.211| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 4.40 r_work: 0.2972 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10489 Z= 0.114 Angle : 0.566 7.633 14228 Z= 0.289 Chirality : 0.040 0.154 1608 Planarity : 0.004 0.062 1831 Dihedral : 6.726 85.554 1447 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.77 % Favored : 94.08 % Rotamer: Outliers : 2.14 % Allowed : 20.50 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.19 (0.24), residues: 1300 helix: 1.50 (0.21), residues: 586 sheet: -1.24 (0.45), residues: 123 loop : -0.96 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 607 TYR 0.009 0.001 TYR A 994 PHE 0.012 0.001 PHE A 161 TRP 0.014 0.001 TRP A 418 HIS 0.005 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (10486) covalent geometry : angle 0.56350 / 0.29 (14222) SS BOND : bond 0.00202 / 0.10 ( 3) SS BOND : angle 2.74933 / 1.56 ( 6) hydrogen bonds : bond 0.03678 / 2.53 ( 514) hydrogen bonds : angle 4.67900 / 3.26 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8164 (tp) REVERT: A 588 LEU cc_start: 0.9509 (mp) cc_final: 0.9305 (mm) REVERT: B 87 GLU cc_start: 0.8892 (pm20) cc_final: 0.8646 (pm20) REVERT: B 275 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7934 (mp0) outliers start: 24 outliers final: 19 residues processed: 132 average time/residue: 0.1706 time to fit residues: 35.6021 Evaluate side-chains 130 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 38 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 75 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.106026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069164 restraints weight = 87497.749| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.38 r_work: 0.2969 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10489 Z= 0.127 Angle : 0.572 8.268 14228 Z= 0.291 Chirality : 0.040 0.157 1608 Planarity : 0.004 0.061 1831 Dihedral : 6.547 82.906 1446 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer: Outliers : 2.14 % Allowed : 20.59 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.20 (0.24), residues: 1300 helix: 1.57 (0.21), residues: 580 sheet: -1.37 (0.45), residues: 128 loop : -0.96 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 607 TYR 0.010 0.001 TYR A 994 PHE 0.011 0.001 PHE A 244 TRP 0.017 0.001 TRP A 418 HIS 0.005 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10486) covalent geometry : angle 0.56927 / 0.29 (14222) SS BOND : bond 0.00121 / 0.06 ( 3) SS BOND : angle 2.74003 / 1.55 ( 6) hydrogen bonds : bond 0.03627 / 2.50 ( 514) hydrogen bonds : angle 4.65647 / 3.24 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 727 LYS cc_start: 0.9470 (tppt) cc_final: 0.9129 (mtmt) REVERT: A 816 MET cc_start: 0.8830 (mmm) cc_final: 0.8408 (mmt) REVERT: B 87 GLU cc_start: 0.8888 (pm20) cc_final: 0.8627 (pm20) REVERT: B 275 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7950 (mp0) outliers start: 24 outliers final: 21 residues processed: 129 average time/residue: 0.1798 time to fit residues: 36.8271 Evaluate side-chains 131 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 38 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 71 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.104225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067211 restraints weight = 88526.004| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 4.28 r_work: 0.2956 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10489 Z= 0.215 Angle : 0.599 8.318 14228 Z= 0.315 Chirality : 0.040 0.175 1608 Planarity : 0.004 0.062 1831 Dihedral : 6.455 80.184 1446 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.62 % Favored : 93.23 % Rotamer: Outliers : 2.23 % Allowed : 20.41 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.03 (0.23), residues: 1300 helix: 1.42 (0.21), residues: 581 sheet: -1.23 (0.46), residues: 121 loop : -1.13 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 837 TYR 0.014 0.001 TYR A 869 PHE 0.010 0.001 PHE A 161 TRP 0.016 0.001 TRP A 418 HIS 0.005 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (10486) covalent geometry : angle 0.59701 / 0.31 (14222) SS BOND : bond 0.00088 / 0.05 ( 3) SS BOND : angle 2.51838 / 1.42 ( 6) hydrogen bonds : bond 0.03828 / 2.65 ( 514) hydrogen bonds : angle 4.82717 / 3.37 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8191 (tp) REVERT: A 267 MET cc_start: 0.8724 (mmm) cc_final: 0.8442 (mmm) REVERT: B 87 GLU cc_start: 0.8888 (pm20) cc_final: 0.8628 (pm20) REVERT: B 275 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8018 (mp0) outliers start: 25 outliers final: 23 residues processed: 124 average time/residue: 0.1704 time to fit residues: 33.0786 Evaluate side-chains 130 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 51 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.105889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.068970 restraints weight = 87643.708| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 4.36 r_work: 0.2966 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10489 Z= 0.123 Angle : 0.582 8.585 14228 Z= 0.295 Chirality : 0.040 0.162 1608 Planarity : 0.004 0.063 1831 Dihedral : 6.247 82.731 1446 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 2.14 % Allowed : 20.59 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.16 (0.24), residues: 1300 helix: 1.58 (0.21), residues: 580 sheet: -1.43 (0.45), residues: 128 loop : -1.03 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 607 TYR 0.010 0.001 TYR A 994 PHE 0.012 0.001 PHE A 244 TRP 0.017 0.001 TRP A 418 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10486) covalent geometry : angle 0.58007 / 0.29 (14222) SS BOND : bond 0.00153 / 0.08 ( 3) SS BOND : angle 2.21260 / 1.25 ( 6) hydrogen bonds : bond 0.03628 / 2.51 ( 514) hydrogen bonds : angle 4.62791 / 3.22 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4971.24 seconds wall clock time: 85 minutes 35.77 seconds (5135.77 seconds total)