Starting phenix.real_space_refine on Wed Sep 17 13:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9im6_60685/09_2025/9im6_60685.cif Found real_map, /net/cci-nas-00/data/ceres_data/9im6_60685/09_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_60685/09_2025/9im6_60685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9im6_60685/09_2025/9im6_60685.map" model { file = "/net/cci-nas-00/data/ceres_data/9im6_60685/09_2025/9im6_60685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9im6_60685/09_2025/9im6_60685.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.28, per 1000 atoms: 0.25 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: 0.80 Conformation dependent library (CDL) restraints added in 242.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.31 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: 1.40 Time building geometry restraints manager: 1.06 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: 1.130 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- 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= 0.146 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG A 44 TYR 0.013 0.001 TYR A 953 PHE 0.015 0.001 PHE A 176 TRP 0.017 0.001 TRP A 390 HIS 0.006 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9153) covalent geometry : angle 0.61559 (12389) hydrogen bonds : bond 0.14992 ( 577) hydrogen bonds : angle 5.23224 ( 1704) *********************** 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 : 0.352 Fit side-chains REVERT: A 193 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7250 (mtm110) outliers start: 2 outliers final: 1 residues processed: 101 average time/residue: 0.0861 time to fit residues: 12.9627 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 : 0.277 ------------------------------------------------------------------------------- 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 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.0030 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 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 = 0.4109 r_free = 0.4109 target = 0.190412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128802 restraints weight = 9856.145| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.52 r_work: 0.3056 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0819 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= 0.124 Angle : 0.549 8.087 12389 Z= 0.286 Chirality : 0.040 0.166 1394 Planarity : 0.005 0.066 1617 Dihedral : 4.968 85.185 1206 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.22 % Favored : 94.34 % Rotamer: Outliers : 1.72 % Allowed : 22.70 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.26), residues: 1130 helix: 2.16 (0.18), residues: 800 sheet: -1.20 (1.06), residues: 15 loop : -1.60 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1078 TYR 0.013 0.001 TYR A 435 PHE 0.017 0.001 PHE A 176 TRP 0.018 0.001 TRP A 390 HIS 0.006 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9153) covalent geometry : angle 0.54930 (12389) hydrogen bonds : bond 0.03764 ( 577) hydrogen bonds : angle 3.98980 ( 1704) *********************** 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 129 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.344 Fit side-chains REVERT: A 79 MET cc_start: 0.6920 (tpt) cc_final: 0.6504 (tpt) REVERT: A 156 ASP cc_start: 0.8123 (m-30) cc_final: 0.7879 (m-30) REVERT: A 513 LEU cc_start: 0.8111 (mp) cc_final: 0.7910 (mt) REVERT: A 612 MET cc_start: 0.6513 (mmm) cc_final: 0.6188 (mmm) REVERT: A 682 ASP cc_start: 0.6612 (OUTLIER) cc_final: 0.5903 (p0) REVERT: A 1022 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6900 (mt-10) outliers start: 17 outliers final: 7 residues processed: 121 average time/residue: 0.0830 time to fit residues: 14.6770 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 : 0.284 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 1 optimal weight: 0.0470 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.190679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.129095 restraints weight = 9812.434| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.52 r_work: 0.3061 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9153 Z= 0.117 Angle : 0.520 7.309 12389 Z= 0.271 Chirality : 0.039 0.161 1394 Planarity : 0.004 0.053 1617 Dihedral : 4.837 84.396 1206 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.66 % Favored : 93.81 % Rotamer: Outliers : 1.52 % Allowed : 23.10 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.26), residues: 1130 helix: 2.27 (0.19), residues: 795 sheet: -1.18 (0.96), residues: 17 loop : -1.51 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.013 0.001 TYR A 435 PHE 0.009 0.001 PHE A 452 TRP 0.019 0.001 TRP A 390 HIS 0.006 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9153) covalent geometry : angle 0.51989 (12389) hydrogen bonds : bond 0.03536 ( 577) hydrogen bonds : angle 3.87865 ( 1704) *********************** 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 120 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.287 Fit side-chains REVERT: A 79 MET cc_start: 0.6973 (tpt) cc_final: 0.6678 (tpt) REVERT: A 102 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6848 (m-30) REVERT: A 156 ASP cc_start: 0.8080 (m-30) cc_final: 0.7714 (m-30) REVERT: A 513 LEU cc_start: 0.8057 (mp) cc_final: 0.7853 (mt) REVERT: A 682 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.5839 (p0) outliers start: 15 outliers final: 6 residues processed: 115 average time/residue: 0.0840 time to fit residues: 14.0959 Evaluate side-chains 109 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 292 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 479 HIS 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 89 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 106 optimal weight: 30.0000 chunk 42 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.189858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130614 restraints weight = 9890.612| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.95 r_work: 0.3076 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1229 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= 0.122 Angle : 0.521 9.451 12389 Z= 0.270 Chirality : 0.039 0.161 1394 Planarity : 0.004 0.051 1617 Dihedral : 4.751 83.198 1206 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.84 % Favored : 93.72 % Rotamer: Outliers : 2.63 % Allowed : 22.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.26), residues: 1130 helix: 2.31 (0.19), residues: 792 sheet: -1.12 (1.01), residues: 17 loop : -1.52 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 193 TYR 0.014 0.001 TYR A 435 PHE 0.009 0.001 PHE A 452 TRP 0.018 0.001 TRP A 390 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9153) covalent geometry : angle 0.52146 (12389) hydrogen bonds : bond 0.03476 ( 577) hydrogen bonds : angle 3.81190 ( 1704) *********************** 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 132 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.351 Fit side-chains REVERT: A 78 GLN cc_start: 0.7181 (mt0) cc_final: 0.6941 (mp10) REVERT: A 79 MET cc_start: 0.6993 (tpt) cc_final: 0.6723 (tpt) REVERT: A 102 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6874 (m-30) REVERT: A 197 GLN cc_start: 0.7512 (tt0) cc_final: 0.7127 (tp40) REVERT: A 612 MET cc_start: 0.6875 (mmp) cc_final: 0.6490 (mmm) REVERT: A 614 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5327 (t0) REVERT: A 682 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.5840 (p0) outliers start: 26 outliers final: 11 residues processed: 124 average time/residue: 0.0743 time to fit residues: 14.0421 Evaluate side-chains 114 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 808 PHE 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 1 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.188682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126607 restraints weight = 9781.122| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.53 r_work: 0.3025 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1318 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= 0.138 Angle : 0.533 8.385 12389 Z= 0.276 Chirality : 0.040 0.163 1394 Planarity : 0.004 0.051 1617 Dihedral : 4.750 81.920 1206 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.02 % Favored : 93.54 % Rotamer: Outliers : 2.23 % Allowed : 23.00 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.26), residues: 1130 helix: 2.25 (0.18), residues: 792 sheet: -0.98 (1.04), residues: 17 loop : -1.49 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 193 TYR 0.015 0.001 TYR A 435 PHE 0.013 0.001 PHE A 918 TRP 0.018 0.001 TRP A 390 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9153) covalent geometry : angle 0.53257 (12389) hydrogen bonds : bond 0.03642 ( 577) hydrogen bonds : angle 3.81265 ( 1704) *********************** 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 126 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.354 Fit side-chains REVERT: A 102 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: A 197 GLN cc_start: 0.7628 (tt0) cc_final: 0.7228 (tp40) REVERT: A 553 MET cc_start: 0.8618 (tpp) cc_final: 0.8392 (tpt) REVERT: A 612 MET cc_start: 0.6854 (mmp) cc_final: 0.6522 (mmm) REVERT: A 614 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5372 (t0) REVERT: A 682 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.5850 (p0) REVERT: A 894 ARG cc_start: 0.7423 (mmt180) cc_final: 0.7218 (tpp-160) outliers start: 22 outliers final: 11 residues processed: 120 average time/residue: 0.0813 time to fit residues: 14.4100 Evaluate side-chains 113 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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 808 PHE Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1042 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 0.0070 chunk 51 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 A1099 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.190076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128327 restraints weight = 9828.339| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.53 r_work: 0.3020 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1469 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= 0.118 Angle : 0.515 7.223 12389 Z= 0.267 Chirality : 0.039 0.167 1394 Planarity : 0.004 0.050 1617 Dihedral : 4.652 80.501 1204 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.75 % Favored : 93.72 % Rotamer: Outliers : 1.93 % Allowed : 23.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.26), residues: 1130 helix: 2.31 (0.19), residues: 794 sheet: -0.88 (1.08), residues: 17 loop : -1.45 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 193 TYR 0.013 0.001 TYR A 435 PHE 0.010 0.001 PHE A 918 TRP 0.019 0.001 TRP A 390 HIS 0.004 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9153) covalent geometry : angle 0.51497 (12389) hydrogen bonds : bond 0.03350 ( 577) hydrogen bonds : angle 3.76023 ( 1704) *********************** 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 125 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.294 Fit side-chains REVERT: A 78 GLN cc_start: 0.7150 (mt0) cc_final: 0.6897 (mp10) REVERT: A 102 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6925 (m-30) REVERT: A 184 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7145 (tm-30) REVERT: A 197 GLN cc_start: 0.7614 (tt0) cc_final: 0.7224 (tp40) REVERT: A 612 MET cc_start: 0.6861 (mmp) cc_final: 0.6519 (mmm) REVERT: A 614 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5506 (t0) REVERT: A 629 MET cc_start: 0.8307 (mmt) cc_final: 0.7566 (mmt) REVERT: A 682 ASP cc_start: 0.6590 (OUTLIER) cc_final: 0.5819 (p0) outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 0.0847 time to fit residues: 14.7820 Evaluate side-chains 115 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 384 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4084 r_free = 0.4084 target = 0.187911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125787 restraints weight = 9827.048| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.52 r_work: 0.3016 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9153 Z= 0.154 Angle : 0.555 12.524 12389 Z= 0.282 Chirality : 0.041 0.178 1394 Planarity : 0.005 0.050 1617 Dihedral : 4.692 79.426 1204 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.19 % Favored : 93.36 % Rotamer: Outliers : 1.93 % Allowed : 23.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.26), residues: 1130 helix: 2.14 (0.18), residues: 800 sheet: -0.60 (1.24), residues: 15 loop : -1.56 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 193 TYR 0.016 0.001 TYR A 435 PHE 0.010 0.001 PHE A 918 TRP 0.018 0.001 TRP A 390 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9153) covalent geometry : angle 0.55467 (12389) hydrogen bonds : bond 0.03748 ( 577) hydrogen bonds : angle 3.81677 ( 1704) *********************** 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 121 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.244 Fit side-chains REVERT: A 102 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6932 (m-30) REVERT: A 184 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 197 GLN cc_start: 0.7625 (tt0) cc_final: 0.7224 (tp40) REVERT: A 612 MET cc_start: 0.6891 (mmp) cc_final: 0.6569 (mmm) REVERT: A 614 ASP cc_start: 0.6115 (OUTLIER) cc_final: 0.5477 (t0) REVERT: A 682 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.5844 (p0) REVERT: A 1042 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.6394 (t70) outliers start: 19 outliers final: 11 residues processed: 116 average time/residue: 0.0875 time to fit residues: 14.8917 Evaluate side-chains 112 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 151 LEU 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 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 808 PHE 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 80 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 110 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.186860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124520 restraints weight = 9813.319| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.53 r_work: 0.2974 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9153 Z= 0.167 Angle : 0.565 12.143 12389 Z= 0.288 Chirality : 0.041 0.181 1394 Planarity : 0.005 0.051 1617 Dihedral : 4.742 77.699 1204 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.46 % Favored : 93.19 % Rotamer: Outliers : 2.13 % Allowed : 23.61 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.26), residues: 1130 helix: 2.06 (0.18), residues: 800 sheet: -0.62 (1.28), residues: 15 loop : -1.57 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 193 TYR 0.017 0.001 TYR A 435 PHE 0.013 0.001 PHE A 918 TRP 0.017 0.001 TRP A 390 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9153) covalent geometry : angle 0.56477 (12389) hydrogen bonds : bond 0.03945 ( 577) hydrogen bonds : angle 3.85145 ( 1704) *********************** 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 118 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.357 Fit side-chains REVERT: A 102 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: A 184 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7200 (tm-30) REVERT: A 612 MET cc_start: 0.6944 (mmp) cc_final: 0.6614 (mmm) REVERT: A 614 ASP cc_start: 0.6123 (OUTLIER) cc_final: 0.5496 (t0) REVERT: A 629 MET cc_start: 0.8381 (mmt) cc_final: 0.7601 (mmt) REVERT: A 682 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.5859 (p0) REVERT: A 750 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7677 (mt-10) outliers start: 21 outliers final: 11 residues processed: 112 average time/residue: 0.0856 time to fit residues: 14.2163 Evaluate side-chains 108 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 384 MET 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 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 949 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.188317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126350 restraints weight = 9795.019| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.51 r_work: 0.2987 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9153 Z= 0.129 Angle : 0.544 11.730 12389 Z= 0.277 Chirality : 0.040 0.176 1394 Planarity : 0.004 0.050 1617 Dihedral : 4.697 76.651 1204 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.55 % Favored : 93.10 % Rotamer: Outliers : 1.93 % Allowed : 23.71 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.26), residues: 1130 helix: 2.15 (0.18), residues: 800 sheet: -0.57 (1.30), residues: 15 loop : -1.59 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 193 TYR 0.014 0.001 TYR A 435 PHE 0.011 0.001 PHE A 918 TRP 0.018 0.001 TRP A 390 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9153) covalent geometry : angle 0.54369 (12389) hydrogen bonds : bond 0.03580 ( 577) hydrogen bonds : angle 3.80034 ( 1704) *********************** 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 116 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.355 Fit side-chains REVERT: A 102 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: A 184 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7191 (tm-30) REVERT: A 612 MET cc_start: 0.6850 (mmp) cc_final: 0.6529 (mmm) REVERT: A 614 ASP cc_start: 0.6099 (OUTLIER) cc_final: 0.5433 (t0) REVERT: A 629 MET cc_start: 0.8340 (mmt) cc_final: 0.7601 (mmt) REVERT: A 645 MET cc_start: 0.8778 (tpp) cc_final: 0.8368 (tpt) REVERT: A 682 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.5835 (p0) REVERT: A 750 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7644 (mt-10) outliers start: 19 outliers final: 11 residues processed: 111 average time/residue: 0.0860 time to fit residues: 14.1974 Evaluate side-chains 109 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 145 ASN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 384 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.187933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125763 restraints weight = 9830.365| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.52 r_work: 0.2978 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1731 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= 0.145 Angle : 0.560 11.727 12389 Z= 0.285 Chirality : 0.041 0.176 1394 Planarity : 0.004 0.050 1617 Dihedral : 4.721 75.498 1204 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.73 % Favored : 93.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.26), residues: 1130 helix: 2.10 (0.18), residues: 800 sheet: -0.55 (1.30), residues: 15 loop : -1.61 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 193 TYR 0.015 0.001 TYR A 435 PHE 0.012 0.001 PHE A 918 TRP 0.018 0.001 TRP A 390 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9153) covalent geometry : angle 0.56029 (12389) hydrogen bonds : bond 0.03708 ( 577) hydrogen bonds : angle 3.81735 ( 1704) ********************** 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 121 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.447 Fit side-chains REVERT: A 102 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: A 184 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 612 MET cc_start: 0.6865 (mmp) cc_final: 0.6555 (mmm) REVERT: A 614 ASP cc_start: 0.6115 (OUTLIER) cc_final: 0.5488 (t0) REVERT: A 682 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.5807 (p0) REVERT: A 750 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7663 (mt-10) outliers start: 20 outliers final: 13 residues processed: 117 average time/residue: 0.0896 time to fit residues: 15.2331 Evaluate side-chains 111 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 384 MET 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 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 949 VAL 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 75 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 593 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.188604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129982 restraints weight = 9735.128| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.97 r_work: 0.3039 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1798 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= 0.132 Angle : 0.560 13.190 12389 Z= 0.282 Chirality : 0.040 0.174 1394 Planarity : 0.004 0.050 1617 Dihedral : 4.667 74.208 1204 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.64 % Favored : 93.10 % Rotamer: Outliers : 1.82 % Allowed : 23.81 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.26), residues: 1130 helix: 2.14 (0.18), residues: 800 sheet: -0.58 (1.30), residues: 15 loop : -1.60 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 193 TYR 0.014 0.001 TYR A 435 PHE 0.011 0.001 PHE A 918 TRP 0.019 0.001 TRP A 390 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9153) covalent geometry : angle 0.55954 (12389) hydrogen bonds : bond 0.03565 ( 577) hydrogen bonds : angle 3.79992 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.35 seconds wall clock time: 39 minutes 4.08 seconds (2344.08 seconds total)