Starting phenix.real_space_refine on Thu Mar 13 14:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9im6_60685/03_2025/9im6_60685.cif Found real_map, /net/cci-nas-00/data/ceres_data/9im6_60685/03_2025/9im6_60685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9im6_60685/03_2025/9im6_60685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9im6_60685/03_2025/9im6_60685.map" model { file = "/net/cci-nas-00/data/ceres_data/9im6_60685/03_2025/9im6_60685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9im6_60685/03_2025/9im6_60685.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5686 2.51 5 N 1522 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8982 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8651 Classifications: {'peptide': 1095} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 1048} Chain: "B" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 331 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'TRANS': 38} Time building chain proxies: 5.00, per 1000 atoms: 0.56 Number of scatterers: 8982 At special positions: 0 Unit cell: (100.43, 99.6, 118.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1705 8.00 N 1522 7.00 C 5686 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: 2.06 Conformation dependent library (CDL) restraints added in 991.8 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 1 sheets defined 80.0% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 21 through 38 removed outlier: 3.724A pdb=" N GLU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 removed outlier: 4.141A pdb=" N VAL A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 73 through 92 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 100 through 118 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.613A pdb=" N LEU A 151 " --> pdb=" O TRP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 176 removed outlier: 3.585A pdb=" N ARG A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.901A pdb=" N ARG A 208 " --> pdb=" O HIS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 235 through 248 removed outlier: 3.632A pdb=" N TYR A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 266 through 271 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 290 through 308 removed outlier: 3.856A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 315 through 330 removed outlier: 3.721A pdb=" N VAL A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 352 through 369 Processing helix chain 'A' and resid 369 through 385 Proline residue: A 375 - end of helix removed outlier: 4.402A pdb=" N GLU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 403 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 414 through 424 removed outlier: 3.648A pdb=" N ILE A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 450 through 470 removed outlier: 3.665A pdb=" N LYS A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 491 removed outlier: 3.598A pdb=" N GLN A 477 " --> pdb=" O ASN A 473 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 478 " --> pdb=" O GLN A 474 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 498 removed outlier: 4.144A pdb=" N ILE A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) Proline residue: A 498 - end of helix Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 507 through 521 removed outlier: 3.520A pdb=" N MET A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.768A pdb=" N GLN A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 4.515A pdb=" N ASP A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) Proline residue: A 554 - end of helix Processing helix chain 'A' and resid 568 through 592 removed outlier: 5.849A pdb=" N LYS A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLU A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 610 removed outlier: 3.684A pdb=" N ASN A 610 " --> pdb=" O GLN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'A' and resid 620 through 633 removed outlier: 3.991A pdb=" N SER A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.522A pdb=" N GLN A 639 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 653 removed outlier: 3.806A pdb=" N GLY A 646 " --> pdb=" O PRO A 642 " (cutoff:3.500A) Proline residue: A 647 - end of helix removed outlier: 3.523A pdb=" N SER A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.590A pdb=" N GLU A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 692 through 711 Processing helix chain 'A' and resid 712 through 716 removed outlier: 3.643A pdb=" N VAL A 715 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A 716 " --> pdb=" O GLY A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 712 through 716' Processing helix chain 'A' and resid 717 through 726 Processing helix chain 'A' and resid 727 through 731 Processing helix chain 'A' and resid 734 through 753 removed outlier: 3.614A pdb=" N ARG A 738 " --> pdb=" O HIS A 734 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) Proline residue: A 746 - end of helix Processing helix chain 'A' and resid 756 through 776 removed outlier: 4.689A pdb=" N ASP A 769 " --> pdb=" O HIS A 765 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA A 770 " --> pdb=" O PHE A 766 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 798 Processing helix chain 'A' and resid 804 through 833 removed outlier: 3.729A pdb=" N GLN A 826 " --> pdb=" O HIS A 822 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 827 " --> pdb=" O PHE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 872 Processing helix chain 'A' and resid 875 through 890 removed outlier: 4.408A pdb=" N GLN A 881 " --> pdb=" O PRO A 877 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU A 882 " --> pdb=" O TRP A 878 " (cutoff:3.500A) Proline residue: A 884 - end of helix removed outlier: 3.510A pdb=" N ILE A 890 " --> pdb=" O ILE A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 913 Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.863A pdb=" N PHE A 918 " --> pdb=" O PRO A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 removed outlier: 3.847A pdb=" N PHE A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix Processing helix chain 'A' and resid 932 through 934 No H-bonds generated for 'chain 'A' and resid 932 through 934' Processing helix chain 'A' and resid 936 through 953 removed outlier: 3.797A pdb=" N ALA A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 952 " --> pdb=" O GLY A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.694A pdb=" N CYS A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 983 through 1001 Processing helix chain 'A' and resid 1002 through 1005 removed outlier: 3.919A pdb=" N VAL A1005 " --> pdb=" O PRO A1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'A' and resid 1006 through 1018 Proline residue: A1012 - end of helix removed outlier: 3.824A pdb=" N SER A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP A1017 " --> pdb=" O HIS A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1041 removed outlier: 3.712A pdb=" N GLN A1029 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1064 removed outlier: 3.641A pdb=" N ILE A1056 " --> pdb=" O ASN A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1087 Processing helix chain 'A' and resid 1089 through 1098 removed outlier: 3.583A pdb=" N TRP A1093 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1115 Processing sheet with id=AA1, first strand: chain 'A' and resid 658 through 661 removed outlier: 3.786A pdb=" N GLN A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1704 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: 2.52 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3011 1.34 - 1.46: 1724 1.46 - 1.58: 4305 1.58 - 1.70: 1 1.70 - 1.81: 112 Bond restraints: 9153 Sorted by residual: bond pdb=" N ASP A 665 " pdb=" CA ASP A 665 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.27e-02 6.20e+03 5.17e+00 bond pdb=" CB PRO A 271 " pdb=" CG PRO A 271 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.91e+00 bond pdb=" N GLU A 667 " pdb=" CA GLU A 667 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.92e+00 bond pdb=" C HIS A1042 " pdb=" N PRO A1043 " ideal model delta sigma weight residual 1.334 1.364 -0.031 2.34e-02 1.83e+03 1.71e+00 bond pdb=" CB MET A1065 " pdb=" CG MET A1065 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 9148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 12284 2.74 - 5.48: 92 5.48 - 8.22: 10 8.22 - 10.96: 1 10.96 - 13.70: 2 Bond angle restraints: 12389 Sorted by residual: angle pdb=" CA PRO A 271 " pdb=" N PRO A 271 " pdb=" CD PRO A 271 " ideal model delta sigma weight residual 112.00 102.22 9.78 1.40e+00 5.10e-01 4.88e+01 angle pdb=" C LEU A 496 " pdb=" N ILE A 497 " pdb=" CA ILE A 497 " ideal model delta sigma weight residual 120.24 123.39 -3.15 6.30e-01 2.52e+00 2.51e+01 angle pdb=" CB MET A1065 " pdb=" CG MET A1065 " pdb=" SD MET A1065 " ideal model delta sigma weight residual 112.70 126.40 -13.70 3.00e+00 1.11e-01 2.08e+01 angle pdb=" N VAL A 331 " pdb=" CA VAL A 331 " pdb=" C VAL A 331 " ideal model delta sigma weight residual 113.07 106.95 6.12 1.37e+00 5.33e-01 2.00e+01 angle pdb=" C LYS A 872 " pdb=" CA LYS A 872 " pdb=" CB LYS A 872 " ideal model delta sigma weight residual 116.34 110.67 5.67 1.40e+00 5.10e-01 1.64e+01 ... (remaining 12384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4659 18.00 - 36.00: 703 36.00 - 53.99: 187 53.99 - 71.99: 40 71.99 - 89.99: 19 Dihedral angle restraints: 5608 sinusoidal: 2282 harmonic: 3326 Sorted by residual: dihedral pdb=" CA HIS A1042 " pdb=" C HIS A1042 " pdb=" N PRO A1043 " pdb=" CA PRO A1043 " ideal model delta harmonic sigma weight residual -180.00 -150.87 -29.13 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PRO A 39 " pdb=" C PRO A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA VAL A 504 " pdb=" C VAL A 504 " pdb=" N LYS A 505 " pdb=" CA LYS A 505 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 5605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 942 0.034 - 0.068: 339 0.068 - 0.103: 84 0.103 - 0.137: 24 0.137 - 0.171: 5 Chirality restraints: 1394 Sorted by residual: chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA PRO A1043 " pdb=" N PRO A1043 " pdb=" C PRO A1043 " pdb=" CB PRO A1043 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" C PRO A 39 " pdb=" CB PRO A 39 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1391 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 270 " -0.087 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO A 271 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 616 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 617 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1073 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO A1074 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A1074 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1074 " 0.029 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 158 2.69 - 3.25: 8952 3.25 - 3.80: 14246 3.80 - 4.35: 17851 4.35 - 4.90: 30430 Nonbonded interactions: 71637 Sorted by model distance: nonbonded pdb=" OE2 GLU A1025 " pdb=" OG1 THR B 182 " model vdw 2.142 3.040 nonbonded pdb=" ND1 HIS A1042 " pdb=" O LEU A1046 " model vdw 2.163 3.120 nonbonded pdb=" OG SER A 917 " pdb=" OH TYR A 958 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP A 129 " pdb=" ND2 ASN A 175 " model vdw 2.288 3.120 nonbonded pdb=" OD1 ASP A 501 " pdb=" OH TYR A 548 " model vdw 2.297 3.040 ... (remaining 71632 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: 0.890 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.540 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: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 0.111 9153 Z= 0.219 Angle : 0.616 13.695 12389 Z= 0.338 Chirality : 0.039 0.171 1394 Planarity : 0.006 0.125 1617 Dihedral : 18.979 89.990 3442 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.37 % Favored : 93.19 % Rotamer: Outliers : 0.20 % Allowed : 24.32 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1130 helix: 1.70 (0.19), residues: 795 sheet: -1.26 (1.03), residues: 15 loop : -1.58 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 390 HIS 0.006 0.001 HIS A 893 PHE 0.015 0.001 PHE A 176 TYR 0.013 0.001 TYR A 953 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.920 Fit side-chains REVERT: A 193 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7250 (mtm110) REVERT: A 763 MET cc_start: 0.7676 (mmt) cc_final: 0.7395 (mmt) outliers start: 2 outliers final: 1 residues processed: 101 average time/residue: 0.1812 time to fit residues: 27.2421 Evaluate side-chains 98 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.0030 chunk 101 optimal weight: 4.9990 overall best weight: 0.8092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.189487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127890 restraints weight = 9798.325| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.51 r_work: 0.3045 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9153 Z= 0.193 Angle : 0.554 8.385 12389 Z= 0.289 Chirality : 0.040 0.166 1394 Planarity : 0.005 0.071 1617 Dihedral : 4.979 85.301 1206 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.40 % Favored : 94.16 % Rotamer: Outliers : 1.62 % Allowed : 22.90 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1130 helix: 2.11 (0.18), residues: 798 sheet: -1.22 (1.06), residues: 15 loop : -1.57 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 390 HIS 0.006 0.001 HIS A 893 PHE 0.016 0.001 PHE A 176 TYR 0.014 0.001 TYR A 435 ARG 0.003 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.948 Fit side-chains REVERT: A 156 ASP cc_start: 0.8135 (m-30) cc_final: 0.7901 (m-30) REVERT: A 513 LEU cc_start: 0.8118 (mp) cc_final: 0.7917 (mt) REVERT: A 612 MET cc_start: 0.6554 (mmm) cc_final: 0.6229 (mmm) REVERT: A 682 ASP cc_start: 0.6628 (OUTLIER) cc_final: 0.5914 (p0) REVERT: A 1022 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6912 (mt-10) outliers start: 16 outliers final: 7 residues processed: 119 average time/residue: 0.1992 time to fit residues: 34.8139 Evaluate side-chains 111 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 971 ARG Chi-restraints excluded: chain A residue 1042 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 86 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 893 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.190755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129050 restraints weight = 9934.172| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.54 r_work: 0.3060 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9153 Z= 0.164 Angle : 0.519 7.345 12389 Z= 0.271 Chirality : 0.039 0.160 1394 Planarity : 0.004 0.053 1617 Dihedral : 4.851 84.489 1206 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.93 % Favored : 93.54 % Rotamer: Outliers : 1.72 % Allowed : 23.00 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.26), residues: 1130 helix: 2.25 (0.18), residues: 801 sheet: -1.15 (1.09), residues: 15 loop : -1.66 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 390 HIS 0.006 0.001 HIS A 893 PHE 0.009 0.001 PHE A 452 TYR 0.012 0.001 TYR A 435 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.990 Fit side-chains REVERT: A 102 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6793 (m-30) REVERT: A 156 ASP cc_start: 0.8084 (m-30) cc_final: 0.7721 (m-30) REVERT: A 513 LEU cc_start: 0.8064 (mp) cc_final: 0.7858 (mt) REVERT: A 682 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.5835 (p0) outliers start: 17 outliers final: 6 residues processed: 118 average time/residue: 0.1858 time to fit residues: 32.0616 Evaluate side-chains 112 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 1042 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.188555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126691 restraints weight = 9730.152| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.51 r_work: 0.3029 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9153 Z= 0.215 Angle : 0.534 9.855 12389 Z= 0.276 Chirality : 0.040 0.161 1394 Planarity : 0.004 0.051 1617 Dihedral : 4.812 83.473 1206 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.93 % Favored : 93.63 % Rotamer: Outliers : 2.23 % Allowed : 22.90 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1130 helix: 2.21 (0.18), residues: 798 sheet: -1.05 (1.13), residues: 15 loop : -1.66 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 390 HIS 0.005 0.001 HIS A 893 PHE 0.011 0.001 PHE A 918 TYR 0.015 0.001 TYR A 435 ARG 0.005 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.007 Fit side-chains REVERT: A 102 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6902 (m-30) REVERT: A 197 GLN cc_start: 0.7609 (tt0) cc_final: 0.7233 (tp40) REVERT: A 513 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7871 (mt) REVERT: A 553 MET cc_start: 0.8659 (tpp) cc_final: 0.8411 (tpt) REVERT: A 612 MET cc_start: 0.6936 (mmp) cc_final: 0.6560 (mmm) REVERT: A 682 ASP cc_start: 0.6637 (OUTLIER) cc_final: 0.5890 (p0) outliers start: 22 outliers final: 12 residues processed: 115 average time/residue: 0.1956 time to fit residues: 32.9385 Evaluate side-chains 114 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1042 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 GLN A 893 HIS A1099 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122190 restraints weight = 9719.227| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.50 r_work: 0.2959 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9153 Z= 0.349 Angle : 0.598 8.781 12389 Z= 0.309 Chirality : 0.043 0.176 1394 Planarity : 0.005 0.054 1617 Dihedral : 4.970 81.682 1206 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.37 % Favored : 93.19 % Rotamer: Outliers : 2.74 % Allowed : 22.59 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1130 helix: 1.86 (0.18), residues: 801 sheet: -0.93 (1.19), residues: 15 loop : -1.68 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 390 HIS 0.006 0.001 HIS A 430 PHE 0.015 0.002 PHE A 918 TYR 0.019 0.002 TYR A 435 ARG 0.004 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.055 Fit side-chains REVERT: A 102 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6966 (m-30) REVERT: A 513 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7988 (mt) REVERT: A 612 MET cc_start: 0.7044 (mmp) cc_final: 0.6706 (mmm) REVERT: A 614 ASP cc_start: 0.6065 (OUTLIER) cc_final: 0.5415 (t0) REVERT: A 682 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.5872 (p0) REVERT: A 750 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7684 (mt-10) REVERT: B 195 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.6146 (ttp) outliers start: 27 outliers final: 13 residues processed: 119 average time/residue: 0.2078 time to fit residues: 36.3576 Evaluate side-chains 114 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain B residue 195 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.188800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126964 restraints weight = 9679.986| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.51 r_work: 0.3030 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9153 Z= 0.184 Angle : 0.524 7.011 12389 Z= 0.273 Chirality : 0.039 0.167 1394 Planarity : 0.005 0.051 1617 Dihedral : 4.775 79.759 1206 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.64 % Favored : 92.92 % Rotamer: Outliers : 2.33 % Allowed : 22.70 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1130 helix: 2.11 (0.18), residues: 798 sheet: -0.73 (1.25), residues: 15 loop : -1.62 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 390 HIS 0.004 0.001 HIS A 893 PHE 0.010 0.001 PHE A 452 TYR 0.012 0.001 TYR A 435 ARG 0.006 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.908 Fit side-chains REVERT: A 102 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6939 (m-30) REVERT: A 184 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7250 (tm-30) REVERT: A 513 LEU cc_start: 0.8205 (mp) cc_final: 0.7885 (mt) REVERT: A 612 MET cc_start: 0.6881 (mmp) cc_final: 0.6548 (mmm) REVERT: A 614 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.5465 (t0) REVERT: A 645 MET cc_start: 0.8711 (tpp) cc_final: 0.8361 (tpt) REVERT: A 682 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.5828 (p0) REVERT: A 750 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7684 (mt-10) REVERT: A 806 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: A 1042 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6573 (t70) outliers start: 23 outliers final: 8 residues processed: 123 average time/residue: 0.1956 time to fit residues: 35.0028 Evaluate side-chains 110 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 1042 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 109 optimal weight: 0.0010 chunk 70 optimal weight: 0.0050 chunk 105 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 593 GLN A 893 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.189349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132594 restraints weight = 9692.390| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.72 r_work: 0.3096 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9153 Z= 0.165 Angle : 0.534 13.931 12389 Z= 0.271 Chirality : 0.039 0.174 1394 Planarity : 0.004 0.051 1617 Dihedral : 4.669 78.425 1204 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.02 % Favored : 93.54 % Rotamer: Outliers : 2.23 % Allowed : 23.10 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.26), residues: 1130 helix: 2.26 (0.19), residues: 794 sheet: -0.74 (1.14), residues: 17 loop : -1.45 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 390 HIS 0.004 0.001 HIS A 430 PHE 0.009 0.001 PHE A 609 TYR 0.011 0.001 TYR A 435 ARG 0.006 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.084 Fit side-chains REVERT: A 102 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: A 184 GLN cc_start: 0.7543 (tm-30) cc_final: 0.7145 (tm-30) REVERT: A 513 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7863 (mt) REVERT: A 612 MET cc_start: 0.6857 (mmp) cc_final: 0.6536 (mmm) REVERT: A 614 ASP cc_start: 0.6080 (OUTLIER) cc_final: 0.5442 (t0) REVERT: A 629 MET cc_start: 0.8277 (mmt) cc_final: 0.7624 (mmt) REVERT: A 682 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.5805 (p0) REVERT: A 702 MET cc_start: 0.8442 (mmt) cc_final: 0.8132 (mmp) REVERT: A 806 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: A 1042 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.6559 (t70) outliers start: 22 outliers final: 9 residues processed: 119 average time/residue: 0.1941 time to fit residues: 34.6496 Evaluate side-chains 113 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1042 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 593 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.187205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125140 restraints weight = 9950.618| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.53 r_work: 0.2998 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9153 Z= 0.245 Angle : 0.564 13.237 12389 Z= 0.285 Chirality : 0.041 0.184 1394 Planarity : 0.005 0.051 1617 Dihedral : 4.716 77.186 1204 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.19 % Favored : 93.45 % Rotamer: Outliers : 2.33 % Allowed : 23.10 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1130 helix: 2.11 (0.18), residues: 800 sheet: -0.54 (1.30), residues: 15 loop : -1.55 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 390 HIS 0.005 0.001 HIS A 430 PHE 0.012 0.001 PHE A 918 TYR 0.016 0.001 TYR A 435 ARG 0.007 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.899 Fit side-chains REVERT: A 102 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: A 184 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7174 (tm-30) REVERT: A 513 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7879 (mt) REVERT: A 612 MET cc_start: 0.6857 (mmp) cc_final: 0.6544 (mmm) REVERT: A 614 ASP cc_start: 0.6161 (OUTLIER) cc_final: 0.5484 (t0) REVERT: A 645 MET cc_start: 0.8735 (tpp) cc_final: 0.8167 (tpt) REVERT: A 682 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.5846 (p0) REVERT: A 750 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 806 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7191 (tp30) REVERT: A 1042 HIS cc_start: 0.6732 (OUTLIER) cc_final: 0.6503 (t70) outliers start: 23 outliers final: 12 residues processed: 110 average time/residue: 0.1859 time to fit residues: 29.9396 Evaluate side-chains 111 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain B residue 187 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 593 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.187248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125266 restraints weight = 9752.530| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.50 r_work: 0.3028 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9153 Z= 0.240 Angle : 0.568 13.174 12389 Z= 0.286 Chirality : 0.041 0.176 1394 Planarity : 0.004 0.051 1617 Dihedral : 4.731 75.940 1204 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.55 % Favored : 93.19 % Rotamer: Outliers : 2.23 % Allowed : 23.20 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1130 helix: 2.08 (0.18), residues: 800 sheet: -0.59 (1.28), residues: 15 loop : -1.57 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 390 HIS 0.005 0.001 HIS A 430 PHE 0.012 0.001 PHE A 918 TYR 0.015 0.001 TYR A 435 ARG 0.007 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.947 Fit side-chains REVERT: A 102 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6950 (m-30) REVERT: A 184 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7184 (tm-30) REVERT: A 513 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7893 (mt) REVERT: A 612 MET cc_start: 0.6878 (mmp) cc_final: 0.6566 (mmm) REVERT: A 614 ASP cc_start: 0.6133 (OUTLIER) cc_final: 0.5470 (t0) REVERT: A 629 MET cc_start: 0.8329 (mmt) cc_final: 0.7563 (mmt) REVERT: A 645 MET cc_start: 0.8735 (tpp) cc_final: 0.8190 (tpt) REVERT: A 682 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.5849 (p0) REVERT: A 750 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 806 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: A 1042 HIS cc_start: 0.6805 (OUTLIER) cc_final: 0.6586 (t70) outliers start: 22 outliers final: 13 residues processed: 113 average time/residue: 0.1896 time to fit residues: 31.2747 Evaluate side-chains 114 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain B residue 187 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 0.0070 chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 593 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.189179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127360 restraints weight = 9850.344| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.51 r_work: 0.3053 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9153 Z= 0.182 Angle : 0.554 12.682 12389 Z= 0.279 Chirality : 0.039 0.173 1394 Planarity : 0.004 0.051 1617 Dihedral : 4.671 75.044 1204 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.55 % Favored : 93.19 % Rotamer: Outliers : 2.33 % Allowed : 23.20 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1130 helix: 2.18 (0.18), residues: 800 sheet: -0.55 (1.30), residues: 15 loop : -1.64 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 390 HIS 0.004 0.001 HIS A 430 PHE 0.010 0.001 PHE A 918 TYR 0.012 0.001 TYR A 435 ARG 0.008 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.933 Fit side-chains REVERT: A 102 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6898 (m-30) REVERT: A 184 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7154 (tm-30) REVERT: A 410 GLN cc_start: 0.8180 (mp10) cc_final: 0.7971 (mp10) REVERT: A 513 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7920 (mt) REVERT: A 612 MET cc_start: 0.6888 (mmp) cc_final: 0.6571 (mmm) REVERT: A 614 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5447 (t0) REVERT: A 629 MET cc_start: 0.8302 (mmt) cc_final: 0.7594 (mmt) REVERT: A 645 MET cc_start: 0.8695 (tpp) cc_final: 0.8160 (tpt) REVERT: A 682 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.5813 (p0) REVERT: A 702 MET cc_start: 0.8510 (mmt) cc_final: 0.8198 (mmp) REVERT: A 750 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 806 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7154 (tp30) REVERT: A 931 TYR cc_start: 0.8650 (m-80) cc_final: 0.8059 (m-10) REVERT: A 1042 HIS cc_start: 0.6765 (OUTLIER) cc_final: 0.6543 (t70) outliers start: 23 outliers final: 13 residues processed: 123 average time/residue: 0.2177 time to fit residues: 39.1758 Evaluate side-chains 117 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain B residue 187 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 593 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.189113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127328 restraints weight = 9846.627| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.52 r_work: 0.3050 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9153 Z= 0.195 Angle : 0.565 13.570 12389 Z= 0.282 Chirality : 0.040 0.173 1394 Planarity : 0.004 0.051 1617 Dihedral : 4.651 74.406 1204 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.28 % Favored : 93.45 % Rotamer: Outliers : 2.03 % Allowed : 23.40 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.26), residues: 1130 helix: 2.10 (0.18), residues: 806 sheet: -0.50 (1.30), residues: 15 loop : -1.60 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 390 HIS 0.004 0.001 HIS A 430 PHE 0.011 0.001 PHE A 176 TYR 0.013 0.001 TYR A 435 ARG 0.008 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4464.23 seconds wall clock time: 78 minutes 11.61 seconds (4691.61 seconds total)